HEADER OXIDOREDUCTASE 06-MAR-19 6QWQ TITLE STRUCTURE OF GTPEBB COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN BILIN REDUCTASE PLASTID; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GUILLARDIA THETA CCMP2712; SOURCE 3 ORGANISM_TAXID: 905079; SOURCE 4 GENE: GUITHDRAFT_96430; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1-TEV-GTPEBB_CUT70 KEYWDS PHYCOBILIN SYNTHESIS, DIHYDROBILIVERDIN, PHYCOERYTHROBILIN, KEYWDS 2 FERREDOXIN DEPENDENT BILIN REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SOMMERKAMP,E.HOFMANN REVDAT 3 02-OCT-19 6QWQ 1 JRNL REVDAT 2 14-AUG-19 6QWQ 1 JRNL REVDAT 1 07-AUG-19 6QWQ 0 JRNL AUTH J.A.SOMMERKAMP,N.FRANKENBERG-DINKEL,E.HOFMANN JRNL TITL CRYSTAL STRUCTURE OF THE FIRST EUKARYOTIC BILIN JRNL TITL 2 REDUCTASEGTPEBB REVEALS A FLIPPED BINDING MODE OF JRNL TITL 3 DIHYDROBILIVERDIN. JRNL REF J.BIOL.CHEM. V. 294 13889 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31366727 JRNL DOI 10.1074/JBC.RA119.009306 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_3126: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 25795 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1295 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 47.4730 - 3.9518 1.00 2841 151 0.1662 0.1744 REMARK 3 2 3.9518 - 3.1369 1.00 2766 145 0.1802 0.2040 REMARK 3 3 3.1369 - 2.7404 0.99 2753 144 0.2258 0.2828 REMARK 3 4 2.7404 - 2.4899 0.99 2722 143 0.2479 0.2786 REMARK 3 5 2.4899 - 2.3114 0.99 2727 146 0.2458 0.2835 REMARK 3 6 2.3114 - 2.1751 0.99 2692 144 0.2721 0.3151 REMARK 3 7 2.1751 - 2.0662 0.98 2696 141 0.2983 0.3121 REMARK 3 8 2.0662 - 1.9762 0.97 2691 143 0.3048 0.3222 REMARK 3 9 1.9762 - 1.9002 0.97 2612 138 0.3374 0.3101 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.500 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 : 0.006 2291 REMARK 3 ANGLE : 0.777 3109 REMARK 3 CHIRALITY : 0.045 310 REMARK 3 PLANARITY : 0.006 401 REMARK 3 DIHEDRAL : 16.010 1354 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 6QWQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292100991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-16 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 : 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) : 1.00601 REMARK 200 MONOCHROMATOR : NULL 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=20160617 REMARK 200 DATA SCALING SOFTWARE : XSCALE BUILT=20160617 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25797 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 47.458 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3100 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) : 1.97 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: SAD REMARK 200 SOFTWARE USED: PHENIX 1.10.1_2155 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.5, 34.5 % PEG3350, REMARK 280 0.21 M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,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 31.98667 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 15.99333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 31.98667 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 15.99333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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 -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 LYS A 45 REMARK 465 GLY A 46 REMARK 465 LYS A 47 REMARK 465 ARG A 48 REMARK 465 PHE A 147 REMARK 465 PRO A 148 REMARK 465 GLU A 149 REMARK 465 GLU A 150 REMARK 465 ALA A 151 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 OD1 ASP A 6 O HOH A 601 2.03 REMARK 500 O HOH A 685 O HOH A 734 2.08 REMARK 500 O HOH A 680 O HOH A 763 2.11 REMARK 500 O HOH A 605 O HOH A 706 2.17 REMARK 500 O HOH A 762 O HOH A 768 2.17 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 THR A 172 -80.92 -109.49 REMARK 500 PHE A 241 -64.57 -141.49 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 SO4 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 DBREF 6QWQ A 1 273 UNP L1IWQ9 L1IWQ9_GUITH 84 356 SEQADV 6QWQ GLY A -1 UNP L1IWQ9 EXPRESSION TAG SEQADV 6QWQ GLY A 0 UNP L1IWQ9 EXPRESSION TAG SEQRES 1 A 275 GLY GLY SER GLU ALA VAL SER ASP ILE TYR LYS PRO PHE SEQRES 2 A 275 TRP GLU TRP ALA ALA LYS THR ILE LYS GLU ARG LEU GLY SEQRES 3 A 275 ASP ASP LEU VAL SER TYR PRO ILE PRO ASP GLY TYR LEU SEQRES 4 A 275 ARG LYS GLU ALA MET VAL GLY LYS GLY LYS ARG GLU SER SEQRES 5 A 275 LEU ALA TRP THR GLN SER TYR GLY TYR GLN THR LYS LYS SEQRES 6 A 275 MET ARG GLN ILE ARG ALA ALA HIS VAL ASN GLY GLY ALA SEQRES 7 A 275 SER LEU GLN VAL LEU ASN LEU VAL PHE PHE PRO HIS MET SEQRES 8 A 275 ASN TYR ASP LEU PRO PHE LEU GLY LEU ASP LEU VAL THR SEQRES 9 A 275 LEU PRO GLY GLY HIS LEU ILE ALA ILE ASP MET GLN PRO SEQRES 10 A 275 LEU PHE GLN THR GLU GLU TYR LYS LYS LYS TYR ALA GLU SEQRES 11 A 275 PRO CYS MET ASP MET TYR GLN LYS HIS VAL LYS ASN LEU SEQRES 12 A 275 PRO TRP GLY GLY ASP PHE PRO GLU GLU ALA LYS GLN TYR SEQRES 13 A 275 PHE SER PRO VAL PHE LEU TRP THR ARG PRO GLN GLU ASP SEQRES 14 A 275 LYS GLN VAL GLU THR TYR VAL PHE GLU ALA PHE LYS ASP SEQRES 15 A 275 TYR ILE ASN LYS TYR LEU ASP PHE VAL GLU ALA ALA LYS SEQRES 16 A 275 PRO VAL THR ASP PRO ASP HIS LEU ALA ARG ILE ARG GLU SEQRES 17 A 275 ARG GLN LEU SER TYR LEU GLN TYR ARG ALA GLU LYS ASP SEQRES 18 A 275 PRO ALA ARG GLY MET PHE THR ARG MET TYR GLY PRO GLU SEQRES 19 A 275 TRP THR GLU ARG TYR ILE HIS GLY PHE LEU PHE ASP LEU SEQRES 20 A 275 GLU GLU LYS MET GLU SER GLY GLU TYR LYS THR GLY GLU SEQRES 21 A 275 LEU LEU PRO CYS SER ASP PRO LEU ASN PHE GLN PRO THR SEQRES 22 A 275 PRO LEU HET SO4 A 500 5 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *168(H2 O) HELIX 1 AA1 TYR A 8 LEU A 23 1 16 HELIX 2 AA2 THR A 119 ALA A 127 1 9 HELIX 3 AA3 CYS A 130 LYS A 139 1 10 HELIX 4 AA4 GLU A 166 THR A 172 1 7 HELIX 5 AA5 THR A 172 ALA A 192 1 21 HELIX 6 AA6 ASP A 197 ASP A 219 1 23 HELIX 7 AA7 PRO A 220 GLY A 230 1 11 HELIX 8 AA8 GLY A 230 PHE A 241 1 12 HELIX 9 AA9 ASP A 244 SER A 251 1 8 SHEET 1 AA1 3 VAL A 28 SER A 29 0 SHEET 2 AA1 3 SER A 50 GLN A 60 -1 O GLN A 60 N VAL A 28 SHEET 3 AA1 3 ARG A 38 VAL A 43 -1 N ALA A 41 O ALA A 52 SHEET 1 AA2 7 VAL A 28 SER A 29 0 SHEET 2 AA2 7 SER A 50 GLN A 60 -1 O GLN A 60 N VAL A 28 SHEET 3 AA2 7 MET A 64 ASN A 73 -1 O HIS A 71 N GLN A 55 SHEET 4 AA2 7 GLN A 79 PRO A 87 -1 O VAL A 80 N VAL A 72 SHEET 5 AA2 7 LEU A 96 THR A 102 -1 O THR A 102 N GLN A 79 SHEET 6 AA2 7 HIS A 107 ASP A 112 -1 O ASP A 112 N GLY A 97 SHEET 7 AA2 7 LEU A 160 THR A 162 -1 O LEU A 160 N ILE A 111 SITE 1 AC1 4 TRP A 14 LYS A 179 HOH A 639 HOH A 704 SITE 1 AC2 1 LYS A 184 SITE 1 AC3 2 ARG A 227 MET A 228 SITE 1 AC4 4 LYS A 20 PHE A 268 HOH A 606 HOH A 633 CRYST1 109.600 109.600 47.980 90.00 90.00 120.00 P 62 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 0.009124 0.005268 0.000000 0.00000 SCALE2 0.000000 0.010536 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020842 0.00000