HEADER OXIDOREDUCTASE 10-MAY-14 4QCD TITLE NEUTRON CRYSTAL STRUCTURE OF PHYCOCYANOBILIN:FERREDOXIN OXIDOREDUCTASE TITLE 2 IN COMPLEX WITH BILIVERDIN IXALPHA AT 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.; SOURCE 3 ORGANISM_TAXID: 1111708; SOURCE 4 STRAIN: PCC 6803; SOURCE 5 GENE: PCYA, SLR0116; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BILIN REDUCTASE, BILIVERDIN IXALPHA, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR M.UNNO,K.ISHIKAWA-SUTO,M.ISHIHARA,Y.HAGIWARA,M.SUGISHIMA,K.WADA, AUTHOR 2 K.FUKUYAMA REVDAT 5 20-MAR-24 4QCD 1 REMARK REVDAT 4 09-JUN-21 4QCD 1 REMARK FORMUL REVDAT 3 04-APR-18 4QCD 1 JRNL REMARK REVDAT 2 24-JAN-18 4QCD 1 REMARK REVDAT 1 29-APR-15 4QCD 0 JRNL AUTH M.UNNO,K.ISHIKAWA-SUTO,K.KUSAKA,T.TAMADA,Y.HAGIWARA, JRNL AUTH 2 M.SUGISHIMA,K.WADA,T.YAMADA,K.TOMOYORI,T.HOSOYA,I.TANAKA, JRNL AUTH 3 N.NIIMURA,R.KUROKI,K.INAKA,M.ISHIHARA,K.FUKUYAMA JRNL TITL INSIGHTS INTO THE PROTON TRANSFER MECHANISM OF A BILIN JRNL TITL 2 REDUCTASE PCYA FOLLOWING NEUTRON CRYSTALLOGRAPHY. JRNL REF J. AM. CHEM. SOC. V. 137 5452 2015 JRNL REFN ESSN 1520-5126 JRNL PMID 25872660 JRNL DOI 10.1021/JACS.5B00645 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 79.4 REMARK 3 NUMBER OF REFLECTIONS : 18379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1839 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 21.1904 - 4.5283 0.85 1466 165 0.1352 0.1916 REMARK 3 2 4.5283 - 3.6000 0.94 1521 169 0.1194 0.1692 REMARK 3 3 3.6000 - 3.1466 0.93 1534 169 0.1354 0.2123 REMARK 3 4 3.1466 - 2.8597 0.93 1491 166 0.1537 0.2188 REMARK 3 5 2.8597 - 2.6551 0.93 1481 165 0.1651 0.2228 REMARK 3 6 2.6551 - 2.4988 0.88 1405 156 0.1616 0.2263 REMARK 3 7 2.4988 - 2.3739 0.85 1341 148 0.1667 0.2064 REMARK 3 8 2.3739 - 2.2706 0.81 1281 144 0.1780 0.2305 REMARK 3 9 2.2706 - 2.1833 0.75 1185 131 0.1845 0.2626 REMARK 3 10 2.1833 - 2.1080 0.72 1153 128 0.2170 0.2744 REMARK 3 11 2.1080 - 2.0422 0.66 1040 116 0.2339 0.2875 REMARK 3 12 2.0422 - 1.9839 0.62 970 107 0.2573 0.3518 REMARK 3 13 1.9839 - 1.9317 0.43 672 75 0.2936 0.3286 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.550 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 : 0.011 4954 REMARK 3 ANGLE : 1.376 8534 REMARK 3 CHIRALITY : 0.060 311 REMARK 3 PLANARITY : 0.006 939 REMARK 3 DIHEDRAL : 23.760 1399 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 43919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.720 REMARK 3 FREE R VALUE TEST SET COUNT : 3829 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 36.9146 - 4.6506 0.94 1524 163 0.1380 0.1464 REMARK 3 2 4.6506 - 3.6924 0.99 1515 165 0.1078 0.1303 REMARK 3 3 3.6924 - 3.2260 1.00 1513 166 0.1291 0.1702 REMARK 3 4 3.2260 - 2.9312 1.00 1513 165 0.1525 0.1677 REMARK 3 5 2.9312 - 2.7211 1.00 1473 162 0.1582 0.1929 REMARK 3 6 2.7211 - 2.5608 1.00 1480 159 0.1528 0.1594 REMARK 3 7 2.5608 - 2.4325 1.00 1494 161 0.1425 0.1495 REMARK 3 8 2.4325 - 2.3267 1.00 1476 157 0.1447 0.1569 REMARK 3 9 2.3267 - 2.2371 1.00 1486 157 0.1434 0.1626 REMARK 3 10 2.2371 - 2.1599 1.00 1460 153 0.1419 0.1729 REMARK 3 11 2.1599 - 2.0924 1.00 1481 152 0.1470 0.1642 REMARK 3 12 2.0924 - 2.0326 1.00 1457 149 0.1449 0.1753 REMARK 3 13 2.0326 - 1.9791 1.00 1488 151 0.1462 0.1695 REMARK 3 14 1.9791 - 1.9308 1.00 1488 140 0.1547 0.1925 REMARK 3 15 1.9308 - 1.8869 1.00 1490 127 0.1541 0.1984 REMARK 3 16 1.8869 - 1.8468 0.99 1503 127 0.1591 0.2113 REMARK 3 17 1.8468 - 1.8098 1.00 1466 123 0.1603 0.1931 REMARK 3 18 1.8098 - 1.7757 0.99 1486 127 0.1593 0.1983 REMARK 3 19 1.7757 - 1.7439 1.00 1490 126 0.1516 0.1922 REMARK 3 20 1.7439 - 1.7144 0.99 1490 126 0.1640 0.1700 REMARK 3 21 1.7144 - 1.6867 1.00 1470 125 0.1679 0.1735 REMARK 3 22 1.6867 - 1.6608 1.00 1468 124 0.1604 0.1796 REMARK 3 23 1.6608 - 1.6364 0.98 1497 126 0.1568 0.2326 REMARK 3 24 1.6364 - 1.6133 1.00 1479 125 0.1594 0.1787 REMARK 3 25 1.6133 - 1.5915 0.98 1460 124 0.1717 0.1976 REMARK 3 26 1.5915 - 1.5708 0.99 1479 125 0.1797 0.2176 REMARK 3 27 1.5708 - 1.5512 0.99 1464 124 0.1916 0.2302 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.260 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 4QCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) 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 : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 10-APR-13 REMARK 230 TEMPERATURE (KELVIN) : 273.0 REMARK 230 PH : 5.90 REMARK 230 NUMBER OF CRYSTALS USED : 1 REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : BL-03 REMARK 230 WAVELENGTH OR RANGE (A) : 3.0-5.6 REMARK 230 MONOCHROMATOR : NEUTRON TIME-OF-FLIGHT REMARK 230 OPTICS : WLS-FIBER-BASED SCINTILLATOR REMARK 230 DETECTOR REMARK 230 REMARK 230 DETECTOR TYPE : NULL REMARK 230 DETECTOR MANUFACTURER : NULL REMARK 230 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 230 DATA SCALING SOFTWARE : HKL-2000 REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 43975 REMARK 230 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 230 RESOLUTION RANGE LOW (A) : 50.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 230 DATA REDUNDANCY : NULL REMARK 230 R MERGE (I) : NULL REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : NULL REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 230 COMPLETENESS FOR SHELL (%) : 100.0 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 : CNS REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, NACL, MES, PH 5.9, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 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 35.55350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.63900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.55350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.63900 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 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 ASP A 5 REMARK 465 LEU A 6 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 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 DE ARG A 166 O HOH A 577 1.59 REMARK 500 O SER A 7 O HOH A 560 2.16 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 71 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = -3.5 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 -110.73 -112.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE LIGAND BLA WAS PROTONATED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BLA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D3O A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D1E RELATED DB: PDB REMARK 900 X-RAY STRUCTURE DBREF 4QCD A 1 248 UNP Q55891 PCYA_SYNY3 1 248 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 ILE 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 BLA A 301 76 HET D3O A 302 4 HETNAM BLA BILIVERDINE IX ALPHA HETNAM D3O TRIDEUTERIOOXIDANIUM HETSYN D3O PERDEUTERATED OXONIUM FORMUL 2 BLA C33 H34 N4 O6 FORMUL 3 D3O D3 O 1+ FORMUL 4 HOH *185(H2 O) HELIX 1 1 LEU A 13 LEU A 17 5 5 HELIX 2 2 ASN A 18 GLN A 33 1 16 HELIX 3 3 LEU A 42 LEU A 46 5 5 HELIX 4 4 PRO A 95 GLY A 98 5 4 HELIX 5 5 PRO A 130 GLY A 141 1 12 HELIX 6 6 PRO A 152 PHE A 158 5 7 HELIX 7 7 ASN A 169 ALA A 194 1 26 HELIX 8 8 SER A 198 GLN A 217 1 20 HELIX 9 9 ASN A 219 GLY A 231 1 13 HELIX 10 10 GLY A 231 VAL A 242 1 12 SHEET 1 A 3 LYS A 38 PRO A 39 0 SHEET 2 A 3 LEU A 58 GLN A 66 -1 O GLN A 66 N LYS A 38 SHEET 3 A 3 TYR A 48 GLY A 51 -1 N VAL A 49 O ILE A 60 SHEET 1 B 7 LYS A 38 PRO A 39 0 SHEET 2 B 7 LEU A 58 GLN A 66 -1 O GLN A 66 N LYS A 38 SHEET 3 B 7 PHE A 70 VAL A 80 -1 O LEU A 77 N GLU A 61 SHEET 4 B 7 LEU A 84 PRO A 93 -1 O PHE A 92 N LYS A 72 SHEET 5 B 7 LEU A 101 GLY A 109 -1 O ALA A 108 N ASP A 85 SHEET 6 B 7 GLY A 112 SER A 121 -1 O SER A 121 N LEU A 101 SHEET 7 B 7 LEU A 163 ILE A 165 -1 O LEU A 163 N ALA A 118 SITE 1 AC1 21 SER A 34 GLU A 76 ILE A 86 HIS A 88 SITE 2 AC1 21 VAL A 90 GLY A 103 ASP A 105 SER A 114 SITE 3 AC1 21 ALA A 115 ILE A 117 ARG A 149 ASN A 219 SITE 4 AC1 21 LYS A 221 THR A 222 PHE A 244 HOH A 408 SITE 5 AC1 21 HOH A 433 HOH A 459 HOH A 478 HOH A 522 SITE 6 AC1 21 HOH A 571 SITE 1 AC2 4 HIS A 74 HIS A 88 PHE A 92 LEU A 243 CRYST1 71.107 97.278 43.174 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 0.014063 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010280 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023162 0.00000