HEADER OXIDOREDUCTASE 23-MAR-10 2X9O TITLE STRUCTURE OF 15, 16- DIHYDROBILIVERDIN:FERREDOXIN TITLE 2 OXIDOREDUCTASE (PEBA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 15,16-DIHYDROBILIVERDIN-FERREDOXIN OXIDOREDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-236; COMPND 5 EC: 1.3.7.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 32052; SOURCE 4 STRAIN: WH8020; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-3 KEYWDS PHYCOBILIN SYNTHESIS, CYANOBACTERIA, OXIDOREDUCTASE, KEYWDS 2 PHYCOERYTHROBILIN EXPDTA X-RAY DIFFRACTION AUTHOR A.W.U.BUSCH,N.FRANKENBERG-DINKEL,E.HOFMANN REVDAT 2 13-NOV-13 2X9O 1 COMPND JRNL REMARK VERSN REVDAT 1 30-MAR-11 2X9O 0 JRNL AUTH A.W.U.BUSCH,E.J.REIJERSE,W.LUBITZ,N.FRANKENBERG-DINKEL, JRNL AUTH 2 E.HOFMANN JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHT INTO THE FERREDOXIN- JRNL TITL 2 MEDIATED TWO-ELECTRON REDUCTION OF BILINS. JRNL REF BIOCHEM.J. V. 439 257 2011 JRNL REFN ISSN 0264-6021 JRNL PMID 21729003 JRNL DOI 10.1042/BJ20110814 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT 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 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) : 40.185 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.00 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.68 REMARK 3 NUMBER OF REFLECTIONS : 33086 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.1813 REMARK 3 R VALUE (WORKING SET) : 0.1791 REMARK 3 FREE R VALUE : 0.2247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1655 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 40.1986 - 3.5476 1.00 2703 143 0.1573 0.1902 REMARK 3 2 3.5476 - 2.8161 0.99 2647 139 0.1671 0.2155 REMARK 3 3 2.8161 - 2.4601 0.99 2616 138 0.1837 0.2419 REMARK 3 4 2.4601 - 2.2352 1.00 2599 137 0.1757 0.2139 REMARK 3 5 2.2352 - 2.0750 1.00 2618 137 0.1786 0.2370 REMARK 3 6 2.0750 - 1.9527 1.00 2630 139 0.1800 0.2297 REMARK 3 7 1.9527 - 1.8549 1.00 2610 137 0.1890 0.2427 REMARK 3 8 1.8549 - 1.7742 1.00 2608 137 0.1836 0.2370 REMARK 3 9 1.7742 - 1.7059 1.00 2587 137 0.1920 0.2377 REMARK 3 10 1.7059 - 1.6470 1.00 2592 136 0.2041 0.2448 REMARK 3 11 1.6470 - 1.5955 1.00 2620 138 0.2141 0.2935 REMARK 3 12 1.5955 - 1.5499 0.99 2601 137 0.2193 0.2554 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 : 0.343 REMARK 3 B_SOL : 40.321 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.17 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.9508 REMARK 3 B22 (A**2) : 2.1651 REMARK 3 B33 (A**2) : -5.1159 REMARK 3 B12 (A**2) : 0.0000 REMARK 3 B13 (A**2) : 1.6075 REMARK 3 B23 (A**2) : -0.0000 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 : 0.007 2038 REMARK 3 ANGLE : 1.164 2773 REMARK 3 CHIRALITY : 0.083 272 REMARK 3 PLANARITY : 0.006 362 REMARK 3 DIHEDRAL : 16.079 728 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: RESIDUES 128 AND 129 WERE NOT MODELLED REMARK 3 DUE TO MISSING DENSITY REMARK 4 REMARK 4 2X9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-MAR-10. REMARK 100 THE PDBE ID CODE IS EBI-43390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978946 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33089 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.55 REMARK 200 RESOLUTION RANGE LOW (A) : 40.18 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.7 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.53 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.2 REMARK 200 R MERGE FOR SHELL (I) : 0.34 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.91 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.0, 25% PEG4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.67500 REMARK 290 SMTRY3 2 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 GLY A -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 ASN A 128 REMARK 465 GLY A 129 REMARK 465 SER A 234 REMARK 465 HIS A 235 REMARK 465 LYS A 236 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 LYS A 34 -42.94 -132.76 REMARK 500 SER A 135 -52.92 -125.68 REMARK 500 ASP A 205 112.10 -34.11 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 BLA A1234 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST METHIONINE HAS BEEN REPLACED BY 9 RESIDUES FROM REMARK 999 THE PLASMID CONSTRUCT DBREF 2X9O A 2 236 UNP Q02189 PEBA_SYNPY 2 236 SEQADV 2X9O GLY A -7 UNP Q02189 EXPRESSION TAG SEQADV 2X9O PRO A -6 UNP Q02189 EXPRESSION TAG SEQADV 2X9O LEU A -5 UNP Q02189 EXPRESSION TAG SEQADV 2X9O GLY A -4 UNP Q02189 EXPRESSION TAG SEQADV 2X9O SER A -3 UNP Q02189 EXPRESSION TAG SEQADV 2X9O PRO A -2 UNP Q02189 EXPRESSION TAG SEQADV 2X9O GLU A -1 UNP Q02189 EXPRESSION TAG SEQADV 2X9O PHE A 0 UNP Q02189 EXPRESSION TAG SEQADV 2X9O ILE A 1 UNP Q02189 EXPRESSION TAG SEQRES 1 A 244 GLY PRO LEU GLY SER PRO GLU PHE ILE PHE ASP SER PHE SEQRES 2 A 244 LEU ASN GLU LEU HIS SER ASP ILE THR LYS ARG GLY GLY SEQRES 3 A 244 SER PRO LEU PRO LEU PRO GLU GLY LEU GLU GLU CYS ARG SEQRES 4 A 244 SER SER LYS SER SER SER VAL ILE GLN SER TRP LEU TRP SEQRES 5 A 244 ASP VAL PRO GLY PHE ARG ARG TRP ARG VAL THR ARG LEU SEQRES 6 A 244 ASP ALA GLY ASP SER LEU GLN VAL PHE ASN SER VAL ALA SEQRES 7 A 244 TYR PRO ASP TYR ASN TYR ASP HIS PRO LEU MSE GLY VAL SEQRES 8 A 244 ASP LEU LEU TRP PHE GLY ALA ARG GLN LYS LEU VAL ALA SEQRES 9 A 244 VAL LEU ASP PHE GLN PRO LEU VAL GLN ASP LYS ASP TYR SEQRES 10 A 244 LEU ASP ARG TYR PHE SER GLY LEU LYS GLU LEU ASN GLN SEQRES 11 A 244 ARG PHE PRO ASP LEU ASN GLY GLU GLU THR MSE ARG SER SEQRES 12 A 244 PHE ASP PRO ASN GLN TYR PHE SER SER TRP LEU LEU PHE SEQRES 13 A 244 CYS ARG GLY GLY ALA GLU GLN ALA ASP LEU SER LEU PRO SEQRES 14 A 244 LYS ALA PHE SER ALA PHE LEU LYS ALA TYR TRP ASP LEU SEQRES 15 A 244 HIS ASP ASN ALA LYS SER ILE PRO SER THR ILE PRO PRO SEQRES 16 A 244 GLU GLU VAL LYS ASN LEU GLN ASP LYS TYR ASP ILE TYR SEQRES 17 A 244 SER ALA GLU ARG ASP PRO ALA HIS GLY LEU PHE THR SER SEQRES 18 A 244 HIS PHE GLY LYS ASP TRP SER ASN ARG PHE LEU HIS GLU SEQRES 19 A 244 PHE LEU PHE PRO ALA SER SER SER HIS LYS MODRES 2X9O MSE A 81 MET SELENOMETHIONINE MODRES 2X9O MSE A 133 MET SELENOMETHIONINE HET MSE A 81 8 HET MSE A 133 8 HET BLA A1234 43 HETNAM MSE SELENOMETHIONINE HETNAM BLA BILIVERDINE IX ALPHA FORMUL 2 MSE 2(C5 H11 N O2 SE) FORMUL 3 BLA C33 H34 N4 O6 FORMUL 4 HOH *322(H2 O) HELIX 1 1 GLU A -1 ARG A 16 1 18 HELIX 2 2 GLY A 89 GLN A 92 5 4 HELIX 3 3 ASP A 106 PHE A 114 1 9 HELIX 4 4 PHE A 114 PHE A 124 1 11 HELIX 5 5 GLY A 152 SER A 159 1 8 HELIX 6 6 SER A 159 LYS A 179 1 21 HELIX 7 7 PRO A 186 ASP A 205 1 20 HELIX 8 8 ALA A 207 GLY A 216 1 10 HELIX 9 9 GLY A 216 PHE A 227 1 12 SHEET 1 AA 2 SER A 19 LEU A 21 0 SHEET 2 AA 2 VAL A 38 ASP A 45 -1 O LEU A 43 N LEU A 21 SHEET 1 AB 2 GLU A 29 ARG A 31 0 SHEET 2 AB 2 VAL A 38 ASP A 45 -1 O ILE A 39 N CYS A 30 SHEET 1 AC 7 LEU A 147 GLY A 151 0 SHEET 2 AC 7 LYS A 93 GLN A 101 -1 O LEU A 94 N GLY A 151 SHEET 3 AC 7 LEU A 80 PHE A 88 -1 O LEU A 80 N GLN A 101 SHEET 4 AC 7 LEU A 63 PRO A 72 -1 O GLN A 64 N TRP A 87 SHEET 5 AC 7 PHE A 49 ALA A 59 -1 N ARG A 50 O TYR A 71 SHEET 6 AC 7 VAL A 38 ASP A 45 -1 O VAL A 38 N ASP A 58 SHEET 7 AC 7 GLU A 29 ARG A 31 -1 O CYS A 30 N ILE A 39 SHEET 1 AD 7 LEU A 147 GLY A 151 0 SHEET 2 AD 7 LYS A 93 GLN A 101 -1 O LEU A 94 N GLY A 151 SHEET 3 AD 7 LEU A 80 PHE A 88 -1 O LEU A 80 N GLN A 101 SHEET 4 AD 7 LEU A 63 PRO A 72 -1 O GLN A 64 N TRP A 87 SHEET 5 AD 7 PHE A 49 ALA A 59 -1 N ARG A 50 O TYR A 71 SHEET 6 AD 7 VAL A 38 ASP A 45 -1 O VAL A 38 N ASP A 58 SHEET 7 AD 7 SER A 19 LEU A 21 -1 O SER A 19 N ASP A 45 LINK C LEU A 80 N MSE A 81 1555 1555 1.33 LINK C MSE A 81 N GLY A 82 1555 1555 1.33 LINK C THR A 132 N MSE A 133 1555 1555 1.33 LINK C MSE A 133 N ARG A 134 1555 1555 1.33 SITE 1 AC1 20 THR A 55 VAL A 65 ASN A 67 VAL A 69 SITE 2 AC1 20 ASP A 84 LEU A 86 VAL A 97 GLN A 101 SITE 3 AC1 20 MSE A 133 ARG A 134 SER A 135 PHE A 136 SITE 4 AC1 20 PHE A 142 ARG A 150 TYR A 197 PRO A 206 SITE 5 AC1 20 ALA A 207 PHE A 211 HOH A2321 HOH A2322 CRYST1 42.420 39.350 71.270 90.00 105.64 90.00 P 1 21 1 2 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 0.023574 0.000000 0.006600 0.00000 SCALE2 0.000000 0.025413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014571 0.00000