HEADER HYDROLASE 28-OCT-15 5EH9 TITLE INDIRECT CONTRIBUTIONS OF MUTATIONS UNDERLIE OPTIMIZATION OF NEW TITLE 2 ENZYME FUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACYL HOMOSERINE LACTONASE AIIA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AHL-LACTONASE AIIA; COMPND 5 EC: 3.1.1.81; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS THURINGIENSIS SUBSP. KURSTAKI; SOURCE 3 ORGANISM_TAXID: 29339; SOURCE 4 GENE: AIIA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS N-ACYL HOMOSERINE LACTONASE FROM BACILLUS THURINGIENSIS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.-S.HONG,C.J.JACKSON,N.TOKURIKI,G.YANG,F.BAIER REVDAT 1 07-SEP-16 5EH9 0 JRNL AUTH G.YANG,N.HONG,F.BAIER,C.J.JACKSON,N.TOKURIKI JRNL TITL CONFORMATIONAL TINKERING DRIVES EVOLUTION OF A PROMISCUOUS JRNL TITL 2 ACTIVITY THROUGH INDIRECT MUTATIONAL EFFECTS. JRNL REF BIOCHEMISTRY V. 55 4583 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 27444875 JRNL DOI 10.1021/ACS.BIOCHEM.6B00561 REMARK 2 REMARK 2 RESOLUTION. 1.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 58033 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) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.153 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3094 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) : 1.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4245 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2007 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 259 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : 1.50000 REMARK 3 B33 (A**2) : -1.18000 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): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.034 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.898 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.980 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2211 ; 0.026 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2084 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2985 ; 2.244 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4843 ; 1.367 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 273 ; 6.837 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;29.144 ;24.949 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 374 ;11.111 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;23.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 329 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2475 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 473 ; 0.015 ; 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): 1065 ; 3.883 ; 2.021 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1064 ; 3.883 ; 2.021 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1347 ; 4.652 ; 3.053 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1348 ; 4.651 ; 3.053 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1146 ; 6.027 ; 2.548 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1147 ; 6.027 ; 2.550 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1639 ; 6.688 ; 3.612 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2627 ; 7.616 ;19.086 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2628 ; 7.615 ;19.104 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4295 ; 6.809 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 87 ;54.800 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4410 ;20.743 ; 5.000 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 REMARK 4 REMARK 4 5EH9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214838. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61128 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 45.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PDB ENTRY 3DHB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 4 K, 20% (V/V) GLYCEROL, REMARK 280 80 MM TRIS-HCL, PH 8.5, 160 MM MGCL2, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 27.25550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.67900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.73650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.67900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.25550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.73650 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 515 O HOH A 588 2.02 REMARK 500 OG SER A 185 O HOH A 401 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 572 O HOH A 591 4545 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A -1 N HIS A -1 CA 0.210 REMARK 500 HIS A -1 CA HIS A -1 C 0.178 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 GLY A -2 N - CA - C ANGL. DEV. = 19.8 DEGREES REMARK 500 HIS A -1 CB - CA - C ANGL. DEV. = -14.1 DEGREES REMARK 500 HIS A -1 N - CA - C ANGL. DEV. = 24.7 DEGREES REMARK 500 LEU A 40 CB - CG - CD1 ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG A 82 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR A 194 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 219 CG - CD - NE ANGL. DEV. = -12.8 DEGREES REMARK 500 CYS A 243 CA - CB - SG ANGL. DEV. = -10.9 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 50 162.44 68.20 REMARK 500 HIS A 133 -22.14 -143.40 REMARK 500 HIS A 133 -23.84 -143.40 REMARK 500 GLU A 136 0.23 -69.72 REMARK 500 GLU A 136 0.23 -66.45 REMARK 500 ILE A 142 44.49 -147.31 REMARK 500 ILE A 190 -136.54 52.56 REMARK 500 PHE A 246 130.18 -39.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 657 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 658 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH A 659 DISTANCE = 8.23 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 104 NE2 REMARK 620 2 HIS A 106 ND1 94.8 REMARK 620 3 HIS A 169 NE2 104.9 94.8 REMARK 620 4 ASP A 191 OD2 86.2 177.0 87.6 REMARK 620 5 HOH A 420 O 120.5 109.3 125.2 67.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 108 OD2 REMARK 620 2 HIS A 109 NE2 85.1 REMARK 620 3 ASP A 191 OD2 165.9 94.5 REMARK 620 4 HIS A 235 NE2 86.7 120.1 105.4 REMARK 620 5 HOH A 420 O 87.3 107.4 79.3 131.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN 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 GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HED A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DHB RELATED DB: PDB DBREF 5EH9 A 2 250 UNP P0CJ63 AHLLA_BACTK 2 250 SEQADV 5EH9 GLY A -2 UNP P0CJ63 EXPRESSION TAG SEQADV 5EH9 HIS A -1 UNP P0CJ63 EXPRESSION TAG SEQADV 5EH9 MET A 0 UNP P0CJ63 EXPRESSION TAG SEQADV 5EH9 ALA A 1 UNP P0CJ63 EXPRESSION TAG SEQADV 5EH9 VAL A 9 UNP P0CJ63 ILE 9 CONFLICT SEQRES 1 A 253 GLY HIS MET ALA THR VAL LYS LYS LEU TYR PHE VAL PRO SEQRES 2 A 253 ALA GLY ARG CYS MET LEU ASP HIS SER SER VAL ASN SER SEQRES 3 A 253 ALA LEU THR PRO GLY LYS LEU LEU ASN LEU PRO VAL TRP SEQRES 4 A 253 CYS TYR LEU LEU GLU THR GLU GLU GLY PRO ILE LEU VAL SEQRES 5 A 253 ASP THR GLY MET PRO GLU SER ALA VAL ASN ASN GLU GLY SEQRES 6 A 253 LEU PHE ASN GLY THR PHE VAL GLU GLY GLN ILE LEU PRO SEQRES 7 A 253 LYS MET THR GLU GLU ASP ARG ILE VAL ASN ILE LEU LYS SEQRES 8 A 253 ARG VAL GLY TYR GLU PRO ASP ASP LEU LEU TYR ILE ILE SEQRES 9 A 253 SER SER HIS LEU HIS PHE ASP HIS ALA GLY GLY ASN GLY SEQRES 10 A 253 ALA PHE THR ASN THR PRO ILE ILE VAL GLN ARG THR GLU SEQRES 11 A 253 TYR GLU ALA ALA LEU HIS ARG GLU GLU TYR MET LYS GLU SEQRES 12 A 253 CYS ILE LEU PRO HIS LEU ASN TYR LYS ILE ILE GLU GLY SEQRES 13 A 253 ASP TYR GLU VAL VAL PRO GLY VAL GLN LEU LEU TYR THR SEQRES 14 A 253 PRO GLY HIS SER PRO GLY HIS GLN SER LEU PHE ILE GLU SEQRES 15 A 253 THR GLU GLN SER GLY SER VAL LEU LEU THR ILE ASP ALA SEQRES 16 A 253 SER TYR THR LYS GLU ASN PHE GLU ASP GLU VAL PRO PHE SEQRES 17 A 253 ALA GLY PHE ASP PRO GLU LEU ALA LEU SER SER ILE LYS SEQRES 18 A 253 ARG LEU LYS GLU VAL VAL LYS LYS GLU LYS PRO ILE ILE SEQRES 19 A 253 PHE PHE GLY HIS ASP ILE GLU GLN GLU LYS SER CYS ARG SEQRES 20 A 253 VAL PHE PRO GLU TYR ILE HET ZN A 301 1 HET ZN A 302 1 HET GOL A 303 6 HET GOL A 304 12 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET HED A 310 8 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM HED 2-HYDROXYETHYL DISULFIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 GOL 7(C3 H8 O3) FORMUL 11 HED C4 H10 O2 S2 FORMUL 12 HOH *259(H2 O) HELIX 1 AA1 SER A 19 VAL A 21 5 3 HELIX 2 AA2 PRO A 54 VAL A 58 5 5 HELIX 3 AA3 THR A 78 ASP A 81 5 4 HELIX 4 AA4 ARG A 82 GLY A 91 1 10 HELIX 5 AA5 GLU A 93 LEU A 97 5 5 HELIX 6 AA6 HIS A 106 GLY A 111 1 6 HELIX 7 AA7 GLY A 112 PHE A 116 5 5 HELIX 8 AA8 ARG A 125 LEU A 132 1 8 HELIX 9 AA9 MET A 138 ILE A 142 5 5 HELIX 10 AB1 ASP A 191 SER A 193 5 3 HELIX 11 AB2 THR A 195 ASP A 201 1 7 HELIX 12 AB3 ASP A 209 LYS A 228 1 20 HELIX 13 AB4 ASP A 236 LYS A 241 1 6 SHEET 1 AA1 7 ILE A 73 LYS A 76 0 SHEET 2 AA1 7 LYS A 5 ASP A 17 -1 N MET A 15 O LEU A 74 SHEET 3 AA1 7 LEU A 30 THR A 42 -1 O CYS A 37 N VAL A 9 SHEET 4 AA1 7 GLY A 45 VAL A 49 -1 O VAL A 49 N TYR A 38 SHEET 5 AA1 7 TYR A 99 ILE A 101 1 O ILE A 101 N LEU A 48 SHEET 6 AA1 7 ILE A 121 GLN A 124 1 O ILE A 122 N ILE A 100 SHEET 7 AA1 7 TYR A 148 ILE A 151 1 O LYS A 149 N ILE A 121 SHEET 1 AA2 5 TYR A 155 VAL A 158 0 SHEET 2 AA2 5 VAL A 161 TYR A 165 -1 O LEU A 163 N TYR A 155 SHEET 3 AA2 5 GLN A 174 THR A 180 -1 O PHE A 177 N GLN A 162 SHEET 4 AA2 5 GLY A 184 ILE A 190 -1 O VAL A 186 N ILE A 178 SHEET 5 AA2 5 ILE A 230 PHE A 233 1 O ILE A 230 N LEU A 187 LINK NE2 HIS A 104 ZN ZN A 302 1555 1555 2.10 LINK ND1 HIS A 106 ZN ZN A 302 1555 1555 2.15 LINK OD2 ASP A 108 ZN ZN A 301 1555 1555 2.25 LINK NE2 HIS A 109 ZN ZN A 301 1555 1555 2.07 LINK NE2 HIS A 169 ZN ZN A 302 1555 1555 2.04 LINK OD2 ASP A 191 ZN ZN A 301 1555 1555 2.03 LINK OD2 ASP A 191 ZN ZN A 302 1555 1555 2.57 LINK NE2 HIS A 235 ZN ZN A 301 1555 1555 2.08 LINK ZN ZN A 301 O HOH A 420 1555 1555 2.02 LINK ZN ZN A 302 O HOH A 420 1555 1555 1.99 CISPEP 1 GLY A -2 HIS A -1 0 -5.09 CISPEP 2 PHE A 246 PRO A 247 0 11.49 SITE 1 AC1 6 ASP A 108 HIS A 109 ASP A 191 HIS A 235 SITE 2 AC1 6 ZN A 302 HOH A 420 SITE 1 AC2 6 HIS A 104 HIS A 106 HIS A 169 ASP A 191 SITE 2 AC2 6 ZN A 301 HOH A 420 SITE 1 AC3 6 LYS A 29 LEU A 30 ARG A 89 PHE A 246 SITE 2 AC3 6 HOH A 417 HOH A 475 SITE 1 AC4 14 MET A 53 GLU A 55 ILE A 83 GLY A 111 SITE 2 AC4 14 GLY A 112 GLY A 114 ALA A 115 GLU A 152 SITE 3 AC4 14 HOH A 409 HOH A 426 HOH A 432 HOH A 467 SITE 4 AC4 14 HOH A 549 HOH A 657 SITE 1 AC5 7 HIS A 145 LEU A 146 ASN A 147 LYS A 226 SITE 2 AC5 7 HOH A 406 HOH A 449 HOH A 543 SITE 1 AC6 6 GLU A 61 GLY A 62 ASN A 65 TYR A 249 SITE 2 AC6 6 HOH A 414 HOH A 555 SITE 1 AC7 5 ASN A 59 GLU A 61 LYS A 76 MET A 77 SITE 2 AC7 5 HOH A 452 SITE 1 AC8 7 HIS A 106 ARG A 134 GLU A 136 HIS A 169 SITE 2 AC8 7 PHE A 208 HOH A 434 HOH A 436 SITE 1 AC9 6 PRO A 94 ALA A 115 GLU A 152 GLY A 153 SITE 2 AC9 6 HOH A 457 HOH A 484 SITE 1 AD1 6 GLU A 136 HOH A 415 HOH A 433 HOH A 434 SITE 2 AD1 6 HOH A 459 HOH A 610 CRYST1 54.511 55.473 79.358 90.00 90.00 90.00 P 21 21 21 4 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 0.018345 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018027 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012601 0.00000 MASTER 421 0 10 13 12 0 22 6 0 0 0 20 END