HEADER OXIDOREDUCTASE 22-JUL-22 7YK9 TITLE NEUTRON STRUCTURE OF PCYA I86D MUTANT COMPLEXED WITH BILIVERDIN AT TITLE 2 ROOM TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHYCOCYANOBILIN:FERREDOXIN OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.3.7.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: PCC 6803; SOURCE 5 GENE: PCYA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHYCOCYANOBILIN, BILIVERDIN, NEUTRON, JOINT-REFINEMENT, ROOM KEYWDS 2 TEMPERATURE, PIGMENT, SUBSTRATE, INACTIVE, ABSORPTION SPECTRUM, KEYWDS 3 HYDROGEN ATOM, PROTON, MUTANT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR M.UNNO,K.IGARASHI REVDAT 2 03-APR-24 7YK9 1 REMARK REVDAT 1 25-JAN-23 7YK9 0 JRNL AUTH T.JOUTSUKA,R.NANASAWA,K.IGARASHI,K.HORIE,M.SUGISHIMA, JRNL AUTH 2 Y.HAGIWARA,K.WADA,K.FUKUYAMA,N.YANO,S.MORI,A.OSTERMANN, JRNL AUTH 3 K.KUSAKA,M.UNNO JRNL TITL NEUTRON CRYSTALLOGRAPHY AND QUANTUM CHEMICAL ANALYSIS OF JRNL TITL 2 BILIN REDUCTASE PCYA MUTANTS REVEAL SUBSTRATE AND CATALYTIC JRNL TITL 3 RESIDUE PROTONATION STATES. JRNL REF J.BIOL.CHEM. V. 299 02763 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36463961 JRNL DOI 10.1016/J.JBC.2022.102763 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 24427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.9100 - 4.5700 1.00 1750 155 0.1334 0.1448 REMARK 3 2 4.5700 - 3.6300 1.00 1634 145 0.0991 0.1288 REMARK 3 3 3.6300 - 3.1700 1.00 1631 146 0.1248 0.1696 REMARK 3 4 3.1700 - 2.8800 1.00 1588 142 0.1430 0.1903 REMARK 3 5 2.8800 - 2.6700 1.00 1626 145 0.1472 0.1835 REMARK 3 6 2.6700 - 2.5200 1.00 1595 142 0.1456 0.1887 REMARK 3 7 2.5200 - 2.3900 1.00 1587 142 0.1423 0.1972 REMARK 3 8 2.3900 - 2.2900 1.00 1589 141 0.1433 0.1727 REMARK 3 9 2.2900 - 2.2000 1.00 1601 143 0.1569 0.2104 REMARK 3 10 2.2000 - 2.1200 1.00 1578 141 0.1610 0.1988 REMARK 3 11 2.1200 - 2.0600 1.00 1569 140 0.1641 0.2183 REMARK 3 12 2.0600 - 2.0000 1.00 1591 141 0.1720 0.2206 REMARK 3 13 2.0000 - 1.9500 1.00 1552 139 0.1866 0.2510 REMARK 3 14 1.9500 - 1.9000 0.97 1537 137 0.2263 0.2913 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 2227 REMARK 3 ANGLE : 1.456 3068 REMARK 3 CHIRALITY : 0.073 326 REMARK 3 PLANARITY : 0.013 491 REMARK 3 DIHEDRAL : 28.821 899 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.1 REMARK 3 NUMBER OF REFLECTIONS : 17648 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.179 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7YK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300030617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-17 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24473 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7140 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 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: REFMAC REMARK 200 STARTING MODEL: 5B4H REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 30-AUG-17 REMARK 230 TEMPERATURE (KELVIN) : 300.0 REMARK 230 PH : NULL REMARK 230 NUMBER OF CRYSTALS USED : NULL REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : BIODIFF REMARK 230 WAVELENGTH OR RANGE (A) : 3.1 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : NULL REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : BIODIFF REMARK 230 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 230 DATA SCALING SOFTWARE : HKL-2000 REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 17734 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 230 RESOLUTION RANGE LOW (A) : 55.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 230 DATA REDUNDANCY : 1.900 REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 6.5320 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 230 COMPLETENESS FOR SHELL (%) : NULL REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : REFMAC REMARK 230 STARTING MODEL: 5B4H REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CHLORIDE, REMARK 280 SODIUM CACODYLATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -X+1/2,Y+1/2,-Z 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 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 -1.000000 0.000000 0.000000 35.66250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.70750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.66250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.70750 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 TOTAL BURIED SURFACE AREA: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 552 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 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 THR A 4 REMARK 465 GLN A 248 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 10 CG OD1 ND2 REMARK 470 GLU A 144 CG CD OE1 OE2 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 DH TYR A 48 OE2 GLU A 50 1.36 REMARK 500 HE ARG A 166 O HOH A 411 1.44 REMARK 500 DE ARG A 166 O HOH A 411 1.44 REMARK 500 OE1 GLN A 207 D2 HOH A 401 1.49 REMARK 500 DZ3 LYS A 221 O HOH A 410 1.53 REMARK 500 HH TYR A 97 O HOH A 414 1.53 REMARK 500 O HOH A 429 D1 HOH A 454 1.54 REMARK 500 DH TYR A 97 O HOH A 414 1.54 REMARK 500 DD2 ASP A 86 OD2 ASP A 105 1.57 REMARK 500 OE1 GLN A 147 D1 HOH A 404 1.60 REMARK 500 OE1 GLN A 207 O HOH A 401 1.79 REMARK 500 O GLY A 83 O HOH A 402 1.92 REMARK 500 OE2 GLU A 76 O HOH A 403 2.03 REMARK 500 OE1 GLN A 147 O HOH A 404 2.17 REMARK 500 OH TYR A 48 OE2 GLU A 50 2.18 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 PHE A 183 CB - CG - CD2 ANGL. DEV. = -4.8 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 LEU A 53 -111.60 -112.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QCD RELATED DB: PDB REMARK 900 RELATED ID: 5B4H RELATED DB: PDB REMARK 900 RELATED ID: 5B4I RELATED DB: PDB REMARK 900 RELATED ID: 5B4J RELATED DB: PDB DBREF 7YK9 A 1 248 UNP Q55891 PCYA_SYNY3 1 248 SEQADV 7YK9 ASP A 86 UNP Q55891 ILE 86 ENGINEERED MUTATION SEQRES 1 A 248 MET ALA VAL THR ASP LEU SER LEU THR ASN SER SER LEU SEQRES 2 A 248 MET PRO THR LEU ASN PRO MET ILE GLN GLN LEU ALA LEU SEQRES 3 A 248 ALA ILE ALA ALA SER TRP GLN SER LEU PRO LEU LYS PRO SEQRES 4 A 248 TYR GLN LEU PRO GLU ASP LEU GLY TYR VAL GLU GLY ARG SEQRES 5 A 248 LEU GLU GLY GLU LYS LEU VAL ILE GLU ASN ARG CYS TYR SEQRES 6 A 248 GLN THR PRO GLN PHE ARG LYS MET HIS LEU GLU LEU ALA SEQRES 7 A 248 LYS VAL GLY LYS GLY LEU ASP ASP LEU HIS CYS VAL MET SEQRES 8 A 248 PHE PRO GLU PRO LEU TYR GLY LEU PRO LEU PHE GLY CYS SEQRES 9 A 248 ASP ILE VAL ALA GLY PRO GLY GLY VAL SER ALA ALA ILE SEQRES 10 A 248 ALA ASP LEU SER PRO THR GLN SER ASP ARG GLN LEU PRO SEQRES 11 A 248 ALA ALA TYR GLN LYS SER LEU ALA GLU LEU GLY GLN PRO SEQRES 12 A 248 GLU PHE GLU GLN GLN ARG GLU LEU PRO PRO TRP GLY GLU SEQRES 13 A 248 ILE PHE SER GLU TYR CYS LEU PHE ILE ARG PRO SER ASN SEQRES 14 A 248 VAL THR GLU GLU GLU ARG PHE VAL GLN ARG VAL VAL ASP SEQRES 15 A 248 PHE LEU GLN ILE HIS CYS HIS GLN SER ILE VAL ALA GLU SEQRES 16 A 248 PRO LEU SER GLU ALA GLN THR LEU GLU HIS ARG GLN GLY SEQRES 17 A 248 GLN ILE HIS TYR CYS GLN GLN GLN GLN LYS ASN ASP LYS SEQRES 18 A 248 THR ARG ARG VAL LEU GLU LYS ALA PHE GLY GLU ALA TRP SEQRES 19 A 248 ALA GLU ARG TYR MET SER GLN VAL LEU PHE ASP VAL ILE SEQRES 20 A 248 GLN HET BLR A 301 76 HETNAM BLR 3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2- HETNAM 2 BLR YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5- HETNAM 3 BLR OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3- HETNAM 4 BLR OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL- HETNAM 5 BLR 1H-PYRROL-3-YL]PROPANOIC ACID HETSYN BLR BILIRUBIN IX ALPHA FORMUL 2 BLR C33 H36 N4 O6 FORMUL 3 HOH *159(H2 O) HELIX 1 AA1 SER A 7 SER A 11 5 5 HELIX 2 AA2 LEU A 13 LEU A 17 5 5 HELIX 3 AA3 ASN A 18 GLN A 33 1 16 HELIX 4 AA4 LEU A 42 LEU A 46 5 5 HELIX 5 AA5 PRO A 95 GLY A 98 5 4 HELIX 6 AA6 PRO A 130 GLY A 141 1 12 HELIX 7 AA7 PRO A 152 PHE A 158 5 7 HELIX 8 AA8 ASN A 169 ALA A 194 1 26 HELIX 9 AA9 SER A 198 GLN A 217 1 20 HELIX 10 AB1 ASN A 219 GLY A 231 1 13 HELIX 11 AB2 GLY A 231 VAL A 242 1 12 SHEET 1 AA1 3 LYS A 38 PRO A 39 0 SHEET 2 AA1 3 LEU A 58 GLN A 66 -1 O GLN A 66 N LYS A 38 SHEET 3 AA1 3 TYR A 48 GLY A 51 -1 N VAL A 49 O ILE A 60 SHEET 1 AA2 7 LYS A 38 PRO A 39 0 SHEET 2 AA2 7 LEU A 58 GLN A 66 -1 O GLN A 66 N LYS A 38 SHEET 3 AA2 7 PHE A 70 VAL A 80 -1 O MET A 73 N TYR A 65 SHEET 4 AA2 7 LEU A 84 PRO A 93 -1 O PHE A 92 N LYS A 72 SHEET 5 AA2 7 LEU A 101 GLY A 109 -1 O ALA A 108 N ASP A 85 SHEET 6 AA2 7 GLY A 112 SER A 121 -1 O SER A 121 N LEU A 101 SHEET 7 AA2 7 LEU A 163 ILE A 165 -1 O LEU A 163 N ALA A 118 CRYST1 71.325 97.415 43.134 90.00 90.00 90.00 P 21 21 2 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 0.014020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023184 0.00000