HEADER OXIDOREDUCTASE 01-SEP-17 5OWG TITLE STRUCTURE OF PCYX_EBK42635 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PCYX_EBK42635; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARINE METAGENOME; SOURCE 3 ORGANISM_TAXID: 408172; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEXPHIPCYX KEYWDS PHYCOBILIN SYNTHESIS, PHYCOERYTHROBILIN, FERREDOXIN DEPENDENT BILIN KEYWDS 2 REDUCTASE, METAGENOMICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SOMMERKAMP,B.LEDERMANN,N.FRANKENBERG-DINKEL,E.HOFMANN REVDAT 4 08-MAY-24 5OWG 1 REMARK REVDAT 3 06-MAR-19 5OWG 1 REMARK REVDAT 2 31-JAN-18 5OWG 1 JRNL REVDAT 1 29-NOV-17 5OWG 0 JRNL AUTH B.LEDERMANN,M.SCHWAN,J.A.SOMMERKAMP,E.HOFMANN,O.BEJA, JRNL AUTH 2 N.FRANKENBERG-DINKEL JRNL TITL EVOLUTION AND MOLECULAR MECHANISM OF FOUR-ELECTRON REDUCING JRNL TITL 2 FERREDOXIN-DEPENDENT BILIN REDUCTASES FROM OCEANIC PHAGES. JRNL REF FEBS J. V. 285 339 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 29156487 JRNL DOI 10.1111/FEBS.14341 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24211 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.303 REMARK 3 R VALUE (WORKING SET) : 0.302 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1225 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 48.4589 - 4.5750 1.00 2553 138 0.2910 0.2931 REMARK 3 2 4.5750 - 3.6317 1.00 2560 139 0.2641 0.2180 REMARK 3 3 3.6317 - 3.1728 1.00 2533 135 0.2980 0.3865 REMARK 3 4 3.1728 - 2.8827 1.00 2579 141 0.3333 0.3764 REMARK 3 5 2.8827 - 2.6761 1.00 2531 134 0.3527 0.3829 REMARK 3 6 2.6761 - 2.5183 1.00 2558 139 0.3450 0.4586 REMARK 3 7 2.5183 - 2.3922 1.00 2580 133 0.3439 0.4557 REMARK 3 8 2.3922 - 2.2881 1.00 2551 135 0.3540 0.4456 REMARK 3 9 2.2881 - 2.2000 1.00 2541 131 0.3704 0.3832 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.330 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 : 0.003 1526 REMARK 3 ANGLE : 0.546 2059 REMARK 3 CHIRALITY : 0.041 216 REMARK 3 PLANARITY : 0.003 267 REMARK 3 DIHEDRAL : 14.550 908 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 5OWG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.0664 REMARK 200 MONOCHROMATOR : SI MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT 20161205 REMARK 200 DATA SCALING SOFTWARE : XSCALE BUILT 20170601 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24230 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 48.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 120.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.21300 REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 36.36 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 3.24300 REMARK 200 FOR SHELL : 0.510 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.12-2829 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS/HCL PH 8.5, 0.05 M REMARK 280 TRIMETHYLAMINE N-OXIDE, 15% (W/V) PEG MME 2000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 45.91333 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 22.95667 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 22.95667 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 45.91333 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 312 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 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 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 TRP A 3 REMARK 465 GLU A 4 REMARK 465 SER A 62 REMARK 465 LYS A 63 REMARK 465 LEU A 104 REMARK 465 LEU A 105 REMARK 465 GLN A 106 REMARK 465 ILE A 116 REMARK 465 GLU A 117 REMARK 465 GLU A 118 REMARK 465 ASN A 119 REMARK 465 LYS A 120 REMARK 465 TRP A 121 REMARK 465 PHE A 122 REMARK 465 LYS A 123 REMARK 465 PRO A 124 REMARK 465 SER A 125 REMARK 465 LYS A 126 REMARK 465 GLU A 127 REMARK 465 ARG A 128 REMARK 465 GLU A 129 REMARK 465 LEU A 130 REMARK 465 PRO A 131 REMARK 465 GLU A 132 REMARK 465 TRP A 133 REMARK 465 ALA A 134 REMARK 465 LYS A 135 REMARK 465 ALA A 136 REMARK 465 ILE A 137 REMARK 465 PHE A 138 REMARK 465 SER A 139 REMARK 465 GLY A 140 REMARK 465 GLY A 141 REMARK 465 MET A 142 REMARK 465 ILE A 143 REMARK 465 ALA A 144 REMARK 465 ALA A 145 REMARK 465 GLY A 146 REMARK 465 ASN A 147 REMARK 465 VAL A 148 REMARK 465 ARG A 149 REMARK 465 GLU A 150 REMARK 465 ASN A 198 REMARK 465 PRO A 199 REMARK 465 HIS A 200 REMARK 465 GLU A 229 REMARK 465 ASN A 230 REMARK 465 GLN A 231 REMARK 465 PRO A 232 REMARK 465 TYR A 233 REMARK 465 LEU A 234 REMARK 465 LYS A 235 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 MET A 160 H ASN A 164 1.55 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 ARG A 60 58.48 -103.76 REMARK 500 PRO A 81 -168.05 -71.04 REMARK 500 ALA A 89 -52.04 -142.15 REMARK 500 LYS A 92 -13.47 78.68 REMARK 500 HIS A 99 134.51 -170.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 5OWG A -7 235 PDB 5OWG 5OWG -7 235 SEQRES 1 A 243 GLY PRO LEU GLY SER PRO GLU PHE MET ILE TRP GLU ARG SEQRES 2 A 243 LEU ILE LYS TRP LYS ASP GLU THR ILE GLU VAL LEU ASN SEQRES 3 A 243 ASN ASN LEU VAL GLU TYR ASN GLU PRO GLY MET GLU ARG SEQRES 4 A 243 PHE ASN ASN GLU LYS LEU GLY TRP VAL ASN ARG THR TRP SEQRES 5 A 243 ASN ASN ARG TYR ILE ARG ARG ALA HIS LEU ASP VAL VAL SEQRES 6 A 243 ASP VAL ARG GLU SER LYS GLY LEU TRP MET ALA HIS LEU SEQRES 7 A 243 CYS LEU PHE PRO MET LEU THR ASN GLY GLY PRO ILE TYR SEQRES 8 A 243 GLY PHE ASP ILE ILE ALA GLY GLU LYS LYS VAL THR GLY SEQRES 9 A 243 ALA PHE HIS ASP PHE SER PRO LEU LEU GLN LYS ASP HIS SEQRES 10 A 243 PRO LEU THR LYS TRP PHE ILE GLU GLU ASN LYS TRP PHE SEQRES 11 A 243 LYS PRO SER LYS GLU ARG GLU LEU PRO GLU TRP ALA LYS SEQRES 12 A 243 ALA ILE PHE SER GLY GLY MET ILE ALA ALA GLY ASN VAL SEQRES 13 A 243 ARG GLU GLU ASP GLU LEU ASN LYS ILE CYS THR MET ALA SEQRES 14 A 243 VAL SER ASN LEU ASN ASN TYR ILE ASP LYS ILE ARG ASN SEQRES 15 A 243 HIS GLU GLY GLU ALA GLU MET ALA ASP VAL ILE LYS ALA SEQRES 16 A 243 GLN ASN TYR TYR SER GLU HIS GLN GLN LYS ASN PRO HIS SEQRES 17 A 243 THR PRO ARG VAL MET GLN SER LEU GLY LEU PRO GLU GLU SEQRES 18 A 243 ASP ILE LYS LEU PHE CYS SER ASP ASN LEU PHE PRO PHE SEQRES 19 A 243 VAL SER GLU ASN GLN PRO TYR LEU LYS FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 ARG A 5 LEU A 21 1 17 HELIX 2 AA2 GLY A 28 ASN A 33 5 6 HELIX 3 AA3 HIS A 109 TRP A 114 1 6 HELIX 4 AA4 ASP A 152 ILE A 172 1 21 HELIX 5 AA5 ARG A 173 GLU A 176 5 4 HELIX 6 AA6 GLU A 180 LYS A 197 1 18 HELIX 7 AA7 PRO A 202 LEU A 208 1 7 HELIX 8 AA8 PRO A 211 ASN A 222 1 12 SHEET 1 AA1 6 VAL A 22 TYR A 24 0 SHEET 2 AA1 6 TRP A 39 ASN A 45 -1 O THR A 43 N TYR A 24 SHEET 3 AA1 6 ILE A 49 VAL A 59 -1 O LEU A 54 N ARG A 42 SHEET 4 AA1 6 LEU A 65 PRO A 74 -1 O HIS A 69 N ASP A 55 SHEET 5 AA1 6 ILE A 82 ILE A 88 -1 O PHE A 85 N LEU A 70 SHEET 6 AA1 6 GLY A 96 SER A 102 -1 O GLY A 96 N ILE A 88 CRYST1 78.710 78.710 68.870 90.00 90.00 120.00 P 32 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 0.012705 0.007335 0.000000 0.00000 SCALE2 0.000000 0.014670 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014520 0.00000