HEADER OXIDOREDUCTASE 06-JAN-15 4XHY TITLE NADH:FMN OXIDOREDUCTASE FROM PARACOCCUS DENITRIFICANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVIN REDUCTASE DOMAIN PROTEIN, FMN-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARACOCCUS DENITRIFICANS PD 1222; SOURCE 3 ORGANISM_TAXID: 318586; SOURCE 4 GENE: PDEN_2689; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NADH, FLAVIN, FLAVINREDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SEDLACEK,T.KLUMPLER,J.MAREK,I.KUCERA REVDAT 7 17-JUL-19 4XHY 1 REMARK REVDAT 6 10-JUL-19 4XHY 1 REMARK REVDAT 5 18-APR-18 4XHY 1 JRNL REMARK REVDAT 4 17-MAY-17 4XHY 1 JRNL REVDAT 3 10-MAY-17 4XHY 1 JRNL REVDAT 2 21-SEP-16 4XHY 1 JRNL REVDAT 1 27-JAN-16 4XHY 0 JRNL AUTH V.SEDLACEK,T.KLUMPLER,J.MAREK,I.KUCERA JRNL TITL BIOCHEMICAL PROPERTIES AND CRYSTAL STRUCTURE OF THE FLAVIN JRNL TITL 2 REDUCTASE FERA FROM PARACOCCUS DENITRIFICANS. JRNL REF MICROBIOL. RES. V.-189 9 2016 JRNL REFN ISSN 0944-5013 JRNL PMID 27296958 JRNL DOI 10.1016/J.MICRES.2016.04.006 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 25671 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1393 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) : 1.53 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1873 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1193 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.74000 REMARK 3 B22 (A**2) : -0.74000 REMARK 3 B33 (A**2) : 2.40000 REMARK 3 B12 (A**2) : -0.37000 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): 0.068 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.125 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1277 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1226 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1757 ; 1.987 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2814 ; 0.932 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 174 ; 6.923 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 53 ;30.368 ;21.132 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 180 ;10.215 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.818 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 201 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1470 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 310 ; 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): 660 ; 1.087 ; 0.758 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 659 ; 1.087 ; 0.757 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 826 ; 1.736 ; 1.132 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 827 ; 1.735 ; 1.133 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 617 ; 1.539 ; 0.966 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 618 ; 1.538 ; 0.966 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 923 ; 2.394 ; 1.380 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1536 ; 5.685 ; 8.482 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1398 ; 4.977 ; 6.907 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 15 A 176 REMARK 3 ORIGIN FOR THE GROUP (A): 5.5309 7.4947 20.5568 REMARK 3 T TENSOR REMARK 3 T11: 0.0395 T22: 0.1691 REMARK 3 T33: 0.1538 T12: -0.0781 REMARK 3 T13: -0.0082 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.9319 L22: 1.0944 REMARK 3 L33: 2.4036 L12: 0.0132 REMARK 3 L13: -0.3253 L23: -0.2545 REMARK 3 S TENSOR REMARK 3 S11: 0.0354 S12: 0.0137 S13: 0.0145 REMARK 3 S21: 0.0273 S22: -0.0749 S23: -0.0896 REMARK 3 S31: -0.0602 S32: 0.1809 S33: 0.0396 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 4XHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205710. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5-7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28207 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 51.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 8.260 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.1200 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, AMMONIUM SULFATE, AMMONIUM REMARK 280 ACETATE, MES, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.55333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 103.10667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 103.10667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.55333 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 51.55333 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 203 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 261 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 SER A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 PRO A 5 REMARK 465 PRO A 6 REMARK 465 ALA A 7 REMARK 465 THR A 8 REMARK 465 ARG A 9 REMARK 465 ASP A 10 REMARK 465 ARG A 11 REMARK 465 LEU A 12 REMARK 465 ALA A 13 REMARK 465 ASP A 14 REMARK 465 THR A 22 REMARK 465 ALA A 23 REMARK 465 GLU A 24 REMARK 465 ASP A 179 REMARK 465 ALA A 180 REMARK 465 GLY A 181 REMARK 465 LEU A 182 REMARK 465 GLU A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 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 265 O HOH A 391 1.79 REMARK 500 O HOH A 438 O HOH A 448 2.00 REMARK 500 O HOH A 348 O HOH A 372 2.01 REMARK 500 O HOH A 235 O HOH A 334 2.02 REMARK 500 O HOH A 208 O HOH A 389 2.14 REMARK 500 O HOH A 334 O HOH A 365 2.14 REMARK 500 O HOH A 208 O HOH A 220 2.17 REMARK 500 O HOH A 246 O HOH A 271 2.19 REMARK 500 O HOH A 438 O HOH A 445 2.19 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 456 O HOH A 456 4555 1.84 REMARK 500 O HOH A 204 O HOH A 356 6555 1.93 REMARK 500 O HOH A 274 O HOH A 418 6655 1.99 REMARK 500 O HOH A 260 O HOH A 399 6655 2.04 REMARK 500 O HOH A 251 O HOH A 274 6665 2.15 REMARK 500 O HOH A 291 O HOH A 300 6555 2.17 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 34 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 34 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 PRO A 127 C - N - CA ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP A 145 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LEU A 154 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -3.2 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 GLN A 110 -133.55 62.74 REMARK 500 ALA A 143 68.23 -154.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 20 ALA A 21 -147.87 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 451 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 452 DISTANCE = 6.51 ANGSTROMS REMARK 525 HOH A 453 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 454 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 455 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 457 DISTANCE = 8.12 ANGSTROMS DBREF 4XHY A 2 181 UNP A1B5I2 A1B5I2_PARDP 2 181 SEQADV 4XHY LEU A 182 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY GLU A 183 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 184 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 185 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 186 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 187 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 188 UNP A1B5I2 EXPRESSION TAG SEQADV 4XHY HIS A 189 UNP A1B5I2 EXPRESSION TAG SEQRES 1 A 188 SER ARG LEU PRO PRO ALA THR ARG ASP ARG LEU ALA ASP SEQRES 2 A 188 GLU ILE THR PHE HIS PRO ALA THR ALA GLU ALA ARG LEU SEQRES 3 A 188 LEU ARG GLU ALA LEU GLY ARG PHE ALA THR GLY VAL THR SEQRES 4 A 188 VAL VAL THR THR ALA GLY PRO GLN GLY PRO LEU GLY MET SEQRES 5 A 188 THR VAL ASN SER PHE SER SER VAL SER LEU GLU PRO PRO SEQRES 6 A 188 LEU VAL LEU TRP CYS PRO ALA ARG THR SER ALA ARG HIS SEQRES 7 A 188 ALA ALA PHE ALA GLU ALA GLY ALA TRP SER VAL HIS VAL SEQRES 8 A 188 LEU GLY SER GLU GLN LEU GLU THR CYS LEU ARG PHE THR SEQRES 9 A 188 ARG GLY GLY ARG GLN PHE GLU GLY LEU ASP THR VAL LEU SEQRES 10 A 188 THR PRO GLU GLY VAL PRO VAL ILE PRO GLY VAL ALA ALA SEQRES 11 A 188 ARG PHE ASP CYS ALA ALA HIS ALA ALA HIS GLU ALA GLY SEQRES 12 A 188 ASP HIS SER VAL LEU ILE GLY ARG VAL LEU ARG VAL THR SEQRES 13 A 188 VAL ALA GLY PRO GLY ASP HIS PRO LEU VAL PHE ALA ALA SEQRES 14 A 188 GLY ARG PHE GLY GLN PHE GLU PRO ASP ALA GLY LEU GLU SEQRES 15 A 188 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *257(H2 O) HELIX 1 AA1 ARG A 26 GLY A 33 1 8 HELIX 2 AA2 ARG A 78 ALA A 85 1 8 HELIX 3 AA3 GLN A 97 PHE A 104 1 8 SHEET 1 AA1 7 GLY A 49 VAL A 55 0 SHEET 2 AA1 7 THR A 40 GLY A 46 -1 N VAL A 42 O MET A 53 SHEET 3 AA1 7 ALA A 87 VAL A 92 -1 O HIS A 91 N VAL A 41 SHEET 4 AA1 7 ALA A 131 ALA A 143 -1 O ALA A 131 N VAL A 92 SHEET 5 AA1 7 HIS A 146 VAL A 158 -1 O THR A 157 N ARG A 132 SHEET 6 AA1 7 LEU A 67 TRP A 70 -1 N VAL A 68 O GLY A 151 SHEET 7 AA1 7 SER A 59 SER A 62 -1 N SER A 59 O LEU A 69 SHEET 1 AA2 2 VAL A 167 ALA A 169 0 SHEET 2 AA2 2 ARG A 172 GLY A 174 -1 O GLY A 174 N VAL A 167 CISPEP 1 GLU A 64 PRO A 65 0 -5.75 CRYST1 43.910 43.910 154.660 90.00 90.00 120.00 P 31 2 1 6 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 0.022774 0.013148 0.000000 0.00000 SCALE2 0.000000 0.026297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006466 0.00000 MASTER 427 0 0 3 9 0 0 6 0 0 0 15 END