HEADER OXIDOREDUCTASE 10-OCT-13 4N5M TITLE CRYSTAL STRUCTURE OF (R)-3-HYDROXYBUTYRYL-COA DEHYDROGENASE FROM TITLE 2 RALSTONIA EUTROPHA IN COMPLEXED WITH ACETOACETYL-COA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETOACETYL-COA REDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: (R)-3-HYDROXYBUTYRYLCOA DEHYDROGENASE; COMPND 5 EC: 1.1.1.36; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RALSTONIA EUTROPHA; SOURCE 3 ORGANISM_TAXID: 381666; SOURCE 4 STRAIN: H16; SOURCE 5 GENE: PHBB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEX HTA KEYWDS ALPHA/BETA STRUCTURE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-E.KIM,S.KIM,K.-J.KIM REVDAT 2 23-APR-14 4N5M 1 JRNL REVDAT 1 11-DEC-13 4N5M 0 JRNL AUTH J.-E.KIM,J.H.CHANG,E.-J.KIM,K.-J.KIM JRNL TITL CRYSTAL STRUCTURE OF (R)-3-HYDROXYBUTYRYL-COA DEHYDROGENASE JRNL TITL 2 PHAB FROM RALSTONIA EUTROPHA JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 443 783 2014 JRNL REFN ISSN 0006-291X JRNL PMID 24211201 JRNL DOI 10.1016/J.BBRC.2013.10.150 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 146641 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7752 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10598 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 551 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 144 REMARK 3 SOLVENT ATOMS : 543 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : 0.57000 REMARK 3 B33 (A**2) : -1.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.00000 REMARK 3 B23 (A**2) : -0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.825 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3911 ; 0.027 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3728 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5294 ; 2.446 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8551 ; 1.048 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 492 ; 5.748 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;33.157 ;24.465 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 641 ;11.723 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.642 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 599 ; 0.175 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4428 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 882 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1971 ; 2.013 ; 1.457 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1970 ; 2.004 ; 1.457 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2462 ; 2.973 ; 2.179 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4N5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-OCT-13. REMARK 100 THE RCSB ID CODE IS RCSB082781. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 151127 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 16.100 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.29500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1Q7B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ETHANOL, CITRATE, LITHIUM SULFATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 69.78500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 69.78500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 69.78500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 69.78500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 69.78500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 69.78500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 69.78500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 69.78500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 20620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 70.62100 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 531 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -23 REMARK 465 SER A -22 REMARK 465 TYR A -21 REMARK 465 TYR A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 ASP A -13 REMARK 465 TYR A -12 REMARK 465 ASP A -11 REMARK 465 ILE A -10 REMARK 465 PRO A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 0 REMARK 465 MET B -23 REMARK 465 SER B -22 REMARK 465 TYR B -21 REMARK 465 TYR B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 ASP B -13 REMARK 465 TYR B -12 REMARK 465 ASP B -11 REMARK 465 ILE B -10 REMARK 465 PRO B -9 REMARK 465 THR B -8 REMARK 465 GLU B -7 REMARK 465 ASN B -6 REMARK 465 LEU B -5 REMARK 465 TYR B -4 REMARK 465 PHE B -3 REMARK 465 GLN B -2 REMARK 465 GLY B -1 REMARK 465 ALA B 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TRP A 44 CZ3 TRP A 44 CH2 0.096 REMARK 500 TYR A 153 CZ TYR A 153 CE2 -0.093 REMARK 500 THR A 205 CB THR A 205 CG2 -0.199 REMARK 500 GLU B 78 CD GLU B 78 OE2 0.068 REMARK 500 PRO B 207 CD PRO B 207 N 0.129 REMARK 500 ILE B 206 C PRO B 207 N -0.117 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 4 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP A 73 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 83 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 ASP A 129 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 210 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 PHE A 237 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 4 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 4 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG B 22 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP B 26 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG B 41 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP B 73 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 93 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 93 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG B 98 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 102 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 102 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP B 106 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP B 110 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 129 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 130 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 134 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR B 185 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 PRO B 207 CA - N - CD ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP B 236 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 54 71.74 -109.27 REMARK 500 VAL A 95 140.46 -176.30 REMARK 500 SER A 139 -139.51 -94.99 REMARK 500 VAL B 95 142.61 -176.43 REMARK 500 SER B 139 -136.20 -96.04 REMARK 500 ALA B 187 83.84 -65.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 102 0.07 SIDE CHAIN REMARK 500 ARG B 102 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Q7B RELATED DB: PDB REMARK 900 RELATED ID: 3VZP RELATED DB: PDB REMARK 900 RELATED ID: 4N5L RELATED DB: PDB REMARK 900 RELATED ID: 4N5N RELATED DB: PDB DBREF 4N5M A 1 246 UNP P14697 PHBB_CUPNH 1 246 DBREF 4N5M B 1 246 UNP P14697 PHBB_CUPNH 1 246 SEQADV 4N5M MET A -23 UNP P14697 EXPRESSION TAG SEQADV 4N5M SER A -22 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR A -21 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR A -20 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -19 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -18 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -17 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -16 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -15 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS A -14 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASP A -13 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR A -12 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASP A -11 UNP P14697 EXPRESSION TAG SEQADV 4N5M ILE A -10 UNP P14697 EXPRESSION TAG SEQADV 4N5M PRO A -9 UNP P14697 EXPRESSION TAG SEQADV 4N5M THR A -8 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLU A -7 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASN A -6 UNP P14697 EXPRESSION TAG SEQADV 4N5M LEU A -5 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR A -4 UNP P14697 EXPRESSION TAG SEQADV 4N5M PHE A -3 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLN A -2 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLY A -1 UNP P14697 EXPRESSION TAG SEQADV 4N5M ALA A 0 UNP P14697 EXPRESSION TAG SEQADV 4N5M MET B -23 UNP P14697 EXPRESSION TAG SEQADV 4N5M SER B -22 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR B -21 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR B -20 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -19 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -18 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -17 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -16 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -15 UNP P14697 EXPRESSION TAG SEQADV 4N5M HIS B -14 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASP B -13 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR B -12 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASP B -11 UNP P14697 EXPRESSION TAG SEQADV 4N5M ILE B -10 UNP P14697 EXPRESSION TAG SEQADV 4N5M PRO B -9 UNP P14697 EXPRESSION TAG SEQADV 4N5M THR B -8 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLU B -7 UNP P14697 EXPRESSION TAG SEQADV 4N5M ASN B -6 UNP P14697 EXPRESSION TAG SEQADV 4N5M LEU B -5 UNP P14697 EXPRESSION TAG SEQADV 4N5M TYR B -4 UNP P14697 EXPRESSION TAG SEQADV 4N5M PHE B -3 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLN B -2 UNP P14697 EXPRESSION TAG SEQADV 4N5M GLY B -1 UNP P14697 EXPRESSION TAG SEQADV 4N5M ALA B 0 UNP P14697 EXPRESSION TAG SEQRES 1 A 270 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 270 ILE PRO THR GLU ASN LEU TYR PHE GLN GLY ALA MET THR SEQRES 3 A 270 GLN ARG ILE ALA TYR VAL THR GLY GLY MET GLY GLY ILE SEQRES 4 A 270 GLY THR ALA ILE CYS GLN ARG LEU ALA LYS ASP GLY PHE SEQRES 5 A 270 ARG VAL VAL ALA GLY CYS GLY PRO ASN SER PRO ARG ARG SEQRES 6 A 270 GLU LYS TRP LEU GLU GLN GLN LYS ALA LEU GLY PHE ASP SEQRES 7 A 270 PHE ILE ALA SER GLU GLY ASN VAL ALA ASP TRP ASP SER SEQRES 8 A 270 THR LYS THR ALA PHE ASP LYS VAL LYS SER GLU VAL GLY SEQRES 9 A 270 GLU VAL ASP VAL LEU ILE ASN ASN ALA GLY ILE THR ARG SEQRES 10 A 270 ASP VAL VAL PHE ARG LYS MET THR ARG ALA ASP TRP ASP SEQRES 11 A 270 ALA VAL ILE ASP THR ASN LEU THR SER LEU PHE ASN VAL SEQRES 12 A 270 THR LYS GLN VAL ILE ASP GLY MET ALA ASP ARG GLY TRP SEQRES 13 A 270 GLY ARG ILE VAL ASN ILE SER SER VAL ASN GLY GLN LYS SEQRES 14 A 270 GLY GLN PHE GLY GLN THR ASN TYR SER THR ALA LYS ALA SEQRES 15 A 270 GLY LEU HIS GLY PHE THR MET ALA LEU ALA GLN GLU VAL SEQRES 16 A 270 ALA THR LYS GLY VAL THR VAL ASN THR VAL SER PRO GLY SEQRES 17 A 270 TYR ILE ALA THR ASP MET VAL LYS ALA ILE ARG GLN ASP SEQRES 18 A 270 VAL LEU ASP LYS ILE VAL ALA THR ILE PRO VAL LYS ARG SEQRES 19 A 270 LEU GLY LEU PRO GLU GLU ILE ALA SER ILE CYS ALA TRP SEQRES 20 A 270 LEU SER SER GLU GLU SER GLY PHE SER THR GLY ALA ASP SEQRES 21 A 270 PHE SER LEU ASN GLY GLY LEU HIS MET GLY SEQRES 1 B 270 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 B 270 ILE PRO THR GLU ASN LEU TYR PHE GLN GLY ALA MET THR SEQRES 3 B 270 GLN ARG ILE ALA TYR VAL THR GLY GLY MET GLY GLY ILE SEQRES 4 B 270 GLY THR ALA ILE CYS GLN ARG LEU ALA LYS ASP GLY PHE SEQRES 5 B 270 ARG VAL VAL ALA GLY CYS GLY PRO ASN SER PRO ARG ARG SEQRES 6 B 270 GLU LYS TRP LEU GLU GLN GLN LYS ALA LEU GLY PHE ASP SEQRES 7 B 270 PHE ILE ALA SER GLU GLY ASN VAL ALA ASP TRP ASP SER SEQRES 8 B 270 THR LYS THR ALA PHE ASP LYS VAL LYS SER GLU VAL GLY SEQRES 9 B 270 GLU VAL ASP VAL LEU ILE ASN ASN ALA GLY ILE THR ARG SEQRES 10 B 270 ASP VAL VAL PHE ARG LYS MET THR ARG ALA ASP TRP ASP SEQRES 11 B 270 ALA VAL ILE ASP THR ASN LEU THR SER LEU PHE ASN VAL SEQRES 12 B 270 THR LYS GLN VAL ILE ASP GLY MET ALA ASP ARG GLY TRP SEQRES 13 B 270 GLY ARG ILE VAL ASN ILE SER SER VAL ASN GLY GLN LYS SEQRES 14 B 270 GLY GLN PHE GLY GLN THR ASN TYR SER THR ALA LYS ALA SEQRES 15 B 270 GLY LEU HIS GLY PHE THR MET ALA LEU ALA GLN GLU VAL SEQRES 16 B 270 ALA THR LYS GLY VAL THR VAL ASN THR VAL SER PRO GLY SEQRES 17 B 270 TYR ILE ALA THR ASP MET VAL LYS ALA ILE ARG GLN ASP SEQRES 18 B 270 VAL LEU ASP LYS ILE VAL ALA THR ILE PRO VAL LYS ARG SEQRES 19 B 270 LEU GLY LEU PRO GLU GLU ILE ALA SER ILE CYS ALA TRP SEQRES 20 B 270 LEU SER SER GLU GLU SER GLY PHE SER THR GLY ALA ASP SEQRES 21 B 270 PHE SER LEU ASN GLY GLY LEU HIS MET GLY HET CAA A 301 54 HET GOL A 302 6 HET GOL A 303 6 HET GOL A 304 6 HET CAA B 301 54 HET GOL B 302 6 HET GOL B 303 6 HET GOL B 304 6 HETNAM CAA ACETOACETYL-COENZYME A HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CAA 2(C25 H40 N7 O18 P3 S) FORMUL 4 GOL 6(C3 H8 O3) FORMUL 11 HOH *543(H2 O) HELIX 1 1 GLY A 13 ASP A 26 1 14 HELIX 2 2 ARG A 40 LEU A 51 1 12 HELIX 3 3 ASP A 64 VAL A 79 1 16 HELIX 4 4 VAL A 96 MET A 100 5 5 HELIX 5 5 THR A 101 LEU A 113 1 13 HELIX 6 6 LEU A 113 GLY A 131 1 19 HELIX 7 7 SER A 140 GLY A 146 1 7 HELIX 8 8 GLN A 150 ALA A 172 1 23 HELIX 9 9 THR A 188 ALA A 193 1 6 HELIX 10 10 ARG A 195 THR A 205 1 11 HELIX 11 11 LEU A 213 SER A 226 1 14 HELIX 12 12 GLY B 13 ASP B 26 1 14 HELIX 13 13 ARG B 40 LEU B 51 1 12 HELIX 14 14 ASP B 64 VAL B 79 1 16 HELIX 15 15 VAL B 96 MET B 100 5 5 HELIX 16 16 THR B 101 LEU B 113 1 13 HELIX 17 17 LEU B 113 GLY B 131 1 19 HELIX 18 18 SER B 140 GLY B 146 1 7 HELIX 19 19 GLN B 150 ALA B 172 1 23 HELIX 20 20 THR B 188 ALA B 193 1 6 HELIX 21 21 ARG B 195 THR B 205 1 11 HELIX 22 22 LEU B 213 SER B 226 1 14 HELIX 23 23 GLU B 227 GLY B 230 5 4 SHEET 1 A 7 ILE A 56 GLU A 59 0 SHEET 2 A 7 ARG A 29 CYS A 34 1 N ALA A 32 O ILE A 56 SHEET 3 A 7 ILE A 5 VAL A 8 1 N ALA A 6 O VAL A 31 SHEET 4 A 7 VAL A 82 ASN A 87 1 O ILE A 86 N TYR A 7 SHEET 5 A 7 GLY A 133 ILE A 138 1 O VAL A 136 N ASN A 87 SHEET 6 A 7 VAL A 176 PRO A 183 1 O ASN A 179 N ASN A 137 SHEET 7 A 7 ASP A 236 LEU A 239 1 O PHE A 237 N SER A 182 SHEET 1 B 7 ILE B 56 GLU B 59 0 SHEET 2 B 7 ARG B 29 CYS B 34 1 N ALA B 32 O ILE B 56 SHEET 3 B 7 ILE B 5 VAL B 8 1 N VAL B 8 O GLY B 33 SHEET 4 B 7 VAL B 82 ASN B 87 1 O ILE B 86 N TYR B 7 SHEET 5 B 7 GLY B 133 ILE B 138 1 O VAL B 136 N LEU B 85 SHEET 6 B 7 VAL B 176 PRO B 183 1 O ASN B 179 N ASN B 137 SHEET 7 B 7 ASP B 236 LEU B 239 1 O PHE B 237 N SER B 182 SITE 1 AC1 19 ASP A 94 GLN A 147 PHE A 148 GLY A 149 SITE 2 AC1 19 GLN A 150 TYR A 153 GLY A 184 TYR A 185 SITE 3 AC1 19 ILE A 186 MET A 190 VAL A 191 ARG A 195 SITE 4 AC1 19 HOH A 497 HOH A 506 HOH A 543 HOH A 548 SITE 5 AC1 19 HOH A 582 HOH A 598 HOH A 612 SITE 1 AC2 5 ASN A 37 THR A 101 ARG A 102 GOL A 303 SITE 2 AC2 5 TRP B 65 SITE 1 AC3 7 ARG A 98 LYS A 99 MET A 100 GOL A 302 SITE 2 AC3 7 HOH A 536 HOH A 630 LYS B 121 SITE 1 AC4 8 GLY A 60 ASN A 61 VAL A 62 THR A 111 SITE 2 AC4 8 HOH A 434 HOH A 539 HOH A 643 HOH A 653 SITE 1 AC5 18 ASP B 94 ASN B 142 GLN B 147 PHE B 148 SITE 2 AC5 18 GLY B 149 GLN B 150 TYR B 153 GLY B 184 SITE 3 AC5 18 TYR B 185 VAL B 191 ARG B 195 ILE B 202 SITE 4 AC5 18 HOH B 506 HOH B 517 HOH B 522 HOH B 534 SITE 5 AC5 18 HOH B 594 HOH B 638 SITE 1 AC6 9 GLN B 3 ARG B 4 ASP B 26 GLY B 27 SITE 2 AC6 9 PHE B 28 HOH B 446 HOH B 508 HOH B 564 SITE 3 AC6 9 HOH B 568 SITE 1 AC7 9 TYR B 7 THR B 9 GLY B 10 GLY B 33 SITE 2 AC7 9 CYS B 34 SER B 58 GLY B 60 HOH B 402 SITE 3 AC7 9 HOH B 654 SITE 1 AC8 3 GLY B 35 ASN B 61 HOH B 654 CRYST1 139.570 139.570 70.621 90.00 90.00 90.00 P 4 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007165 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007165 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014160 0.00000 MASTER 471 0 8 23 14 0 23 6 0 0 0 42 END