HEADER OXIDOREDUCTASE 03-OCT-24 9GYU TITLE FERREDOXIN CNF-LABELLED REDUCED STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN-1, CHLOROPLASTIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FERREDOXIN I,FD I; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: FERREDOXIN WITH TYR 37 REPLACED WITH COMPND 7 CYANOPHENYLALANINE (4CF) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562; SOURCE 5 GENE: PETF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS METALLOPROTEIN IRON-SULFUR CLUSTER ELECTRON TRANSFER, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.B.CARR,J.WEI,K.A.VINCENT REVDAT 3 30-JUL-25 9GYU 1 JRNL REVDAT 2 11-JUN-25 9GYU 1 JRNL REVDAT 1 28-MAY-25 9GYU 0 JRNL AUTH Z.DUAN,J.WEI,S.B.CARR,M.RAMIREZ,R.M.EVANS,P.A.ASH, JRNL AUTH 2 P.RODRIGUEZ-MACIA,A.SACHDEVA,K.A.VINCENT JRNL TITL CYANOPHENYLALANINE AS AN INFRARED PROBE FOR IRON-SULFUR JRNL TITL 2 CLUSTER REDOX STATE IN MULTICENTER METALLOENZYMES. JRNL REF CHEMBIOCHEM V. 26 00251 2025 JRNL REFN ESSN 1439-7633 JRNL PMID 40347495 JRNL DOI 10.1002/CBIC.202500251 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 61312 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 2986 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 31.6900 - 3.0300 1.00 3060 152 0.1466 0.1510 REMARK 3 2 3.0300 - 2.4100 0.99 3000 165 0.1471 0.1540 REMARK 3 3 2.4100 - 2.1000 0.98 3016 143 0.1302 0.1557 REMARK 3 4 2.1000 - 1.9100 0.98 2984 148 0.1288 0.1231 REMARK 3 5 1.9100 - 1.7700 0.97 2972 164 0.1334 0.1483 REMARK 3 6 1.7700 - 1.6700 0.98 2981 154 0.1290 0.1559 REMARK 3 7 1.6700 - 1.5900 0.97 2993 143 0.1329 0.1198 REMARK 3 8 1.5900 - 1.5200 0.99 3012 137 0.1401 0.1865 REMARK 3 9 1.5200 - 1.4600 0.98 3012 148 0.1601 0.1502 REMARK 3 10 1.4600 - 1.4100 0.96 2953 152 0.1700 0.2271 REMARK 3 11 1.4100 - 1.3600 0.96 2911 174 0.1777 0.2066 REMARK 3 12 1.3600 - 1.3300 0.93 2833 145 0.1903 0.1740 REMARK 3 13 1.3300 - 1.2900 0.91 2783 121 0.2101 0.2209 REMARK 3 14 1.2900 - 1.2600 0.89 2672 154 0.2249 0.2358 REMARK 3 15 1.2600 - 1.2300 0.85 2609 148 0.2422 0.2654 REMARK 3 16 1.2300 - 1.2000 0.86 2576 135 0.2602 0.2720 REMARK 3 17 1.2000 - 1.1800 0.81 2490 122 0.2772 0.2696 REMARK 3 18 1.1800 - 1.1600 0.81 2464 113 0.2784 0.3198 REMARK 3 19 1.1600 - 1.1400 0.78 2365 131 0.2792 0.2870 REMARK 3 20 1.1400 - 1.1200 0.77 2352 119 0.3071 0.2927 REMARK 3 21 1.1200 - 1.1000 0.75 2288 118 0.3053 0.2542 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) : 0.085 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.711 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.78 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 : 0.008 853 REMARK 3 ANGLE : 1.038 1171 REMARK 3 CHIRALITY : 0.084 132 REMARK 3 PLANARITY : 0.009 155 REMARK 3 DIHEDRAL : 6.257 125 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 9GYU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61312 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 53.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.4 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 1.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RED RHOMBAHEDRA 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: 100 MM NA K PHOSPHATE PH 7-8 2.6-3.6 M REMARK 280 AMMONIUM SULPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.45800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.69250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.38050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.69250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.45800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.38050 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: 240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 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 SER A 38 -68.83 -144.74 REMARK 500 SER A 38 -77.48 -129.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 101 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 FES A 101 S1 117.9 REMARK 620 3 FES A 101 S2 100.1 102.5 REMARK 620 4 CYS A 44 SG 106.3 109.9 120.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 101 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 FES A 101 S1 112.7 REMARK 620 3 FES A 101 S2 110.6 104.8 REMARK 620 4 CYS A 77 SG 106.7 117.6 104.0 REMARK 620 N 1 2 3 DBREF 9GYU A 1 97 UNP P00221 FER1_SPIOL 51 147 SEQADV 9GYU GLY A -7 UNP P00221 EXPRESSION TAG SEQADV 9GYU PRO A -6 UNP P00221 EXPRESSION TAG SEQADV 9GYU LEU A -5 UNP P00221 EXPRESSION TAG SEQADV 9GYU GLY A -4 UNP P00221 EXPRESSION TAG SEQADV 9GYU SER A -3 UNP P00221 EXPRESSION TAG SEQADV 9GYU PRO A -2 UNP P00221 EXPRESSION TAG SEQADV 9GYU GLU A -1 UNP P00221 EXPRESSION TAG SEQADV 9GYU PHE A 0 UNP P00221 EXPRESSION TAG SEQADV 9GYU 4CF A 37 UNP P00221 TYR 87 ENGINEERED MUTATION SEQRES 1 A 105 GLY PRO LEU GLY SER PRO GLU PHE ALA ALA TYR LYS VAL SEQRES 2 A 105 THR LEU VAL THR PRO THR GLY ASN VAL GLU PHE GLN CYS SEQRES 3 A 105 PRO ASP ASP VAL TYR ILE LEU ASP ALA ALA GLU GLU GLU SEQRES 4 A 105 GLY ILE ASP LEU PRO 4CF SER CYS ARG ALA GLY SER CYS SEQRES 5 A 105 SER SER CYS ALA GLY LYS LEU LYS THR GLY SER LEU ASN SEQRES 6 A 105 GLN ASP ASP GLN SER PHE LEU ASP ASP ASP GLN ILE ASP SEQRES 7 A 105 GLU GLY TRP VAL LEU THR CYS ALA ALA TYR PRO VAL SER SEQRES 8 A 105 ASP VAL THR ILE GLU THR HIS LYS GLU GLU GLU LEU THR SEQRES 9 A 105 ALA HET 4CF A 37 20 HET FES A 101 4 HETNAM 4CF 4-CYANO-L-PHENYLALANINE HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 1 4CF C10 H10 N2 O2 FORMUL 2 FES FE2 S2 FORMUL 3 HOH *138(H2 O) HELIX 1 AA1 TYR A 23 GLU A 31 1 9 HELIX 2 AA2 ASP A 65 GLU A 71 1 7 HELIX 3 AA3 CYS A 77 ALA A 79 5 3 HELIX 4 AA4 LYS A 91 LEU A 95 5 5 SHEET 1 AA1 5 ASN A 13 PRO A 19 0 SHEET 2 AA1 5 ALA A 2 VAL A 8 -1 N VAL A 5 O PHE A 16 SHEET 3 AA1 5 VAL A 85 GLU A 88 1 O VAL A 85 N THR A 6 SHEET 4 AA1 5 ALA A 48 THR A 53 -1 N LYS A 52 O THR A 86 SHEET 5 AA1 5 TRP A 73 LEU A 75 -1 O VAL A 74 N GLY A 49 SHEET 1 AA2 2 LEU A 56 ASN A 57 0 SHEET 2 AA2 2 TYR A 80 PRO A 81 -1 O TYR A 80 N ASN A 57 LINK C PRO A 36 N 4CF A 37 1555 1555 1.33 LINK C 4CF A 37 N ASER A 38 1555 1555 1.32 LINK C 4CF A 37 N BSER A 38 1555 1555 1.33 LINK SG CYS A 39 FE1 FES A 101 1555 1555 2.31 LINK SG CYS A 44 FE1 FES A 101 1555 1555 2.27 LINK SG CYS A 47 FE2 FES A 101 1555 1555 2.30 LINK SG CYS A 77 FE2 FES A 101 1555 1555 2.28 CRYST1 28.916 46.761 63.385 90.00 90.00 90.00 P 21 21 21 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 0.034583 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021385 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015777 0.00000 CONECT 641 654 CONECT 653 655 658 673 674 CONECT 654 641 658 CONECT 655 653 CONECT 656 657 661 CONECT 657 656 CONECT 658 653 654 659 666 CONECT 659 658 660 667 668 CONECT 660 659 662 663 CONECT 661 656 664 665 CONECT 662 660 664 669 CONECT 663 660 665 670 CONECT 664 661 662 671 CONECT 665 661 663 672 CONECT 666 658 CONECT 667 659 CONECT 668 659 CONECT 669 662 CONECT 670 663 CONECT 671 664 CONECT 672 665 CONECT 673 653 CONECT 674 653 CONECT 700 1599 CONECT 774 1599 CONECT 815 1600 CONECT 1294 1600 CONECT 1599 700 774 1601 1602 CONECT 1600 815 1294 1601 1602 CONECT 1601 1599 1600 CONECT 1602 1599 1600 MASTER 254 0 2 4 7 0 0 6 931 1 31 9 END