HEADER OXIDOREDUCTASE 01-OCT-24 9GYD TITLE FERREDOXIN WILD-TYPE -AS-ISOLATED 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: WILD-TYPE FERREDOXIN AS-ISOLATED STATE 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 9GYD 1 JRNL REVDAT 2 11-JUN-25 9GYD 1 JRNL REVDAT 1 28-MAY-25 9GYD 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. 0.92 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) : 0.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 128152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 6333 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 39.4000 - 2.8600 0.96 3939 175 0.1470 0.1557 REMARK 3 2 2.8600 - 2.2700 1.00 4053 236 0.1391 0.1493 REMARK 3 3 2.2700 - 1.9800 1.00 4056 223 0.1182 0.1271 REMARK 3 4 1.9800 - 1.8000 1.00 4095 189 0.1105 0.1235 REMARK 3 5 1.8000 - 1.6700 1.00 4074 221 0.1028 0.1206 REMARK 3 6 1.6700 - 1.5700 1.00 4094 177 0.0895 0.1113 REMARK 3 7 1.5700 - 1.4900 1.00 4043 226 0.0907 0.0989 REMARK 3 8 1.4900 - 1.4300 1.00 4071 206 0.0958 0.1051 REMARK 3 9 1.4300 - 1.3700 1.00 4076 210 0.0977 0.1166 REMARK 3 10 1.3700 - 1.3300 1.00 4075 222 0.0986 0.1054 REMARK 3 11 1.3300 - 1.2900 1.00 4066 224 0.0980 0.1208 REMARK 3 12 1.2900 - 1.2500 1.00 4043 213 0.1003 0.1234 REMARK 3 13 1.2500 - 1.2200 1.00 4068 199 0.1027 0.1181 REMARK 3 14 1.2200 - 1.1900 1.00 4092 199 0.1045 0.1186 REMARK 3 15 1.1900 - 1.1600 1.00 4037 214 0.1040 0.1178 REMARK 3 16 1.1600 - 1.1300 1.00 4098 211 0.1089 0.1078 REMARK 3 17 1.1300 - 1.1100 1.00 4020 242 0.1155 0.1304 REMARK 3 18 1.1100 - 1.0900 1.00 4009 228 0.1160 0.1216 REMARK 3 19 1.0900 - 1.0700 1.00 4089 228 0.1264 0.1480 REMARK 3 20 1.0700 - 1.0500 1.00 4071 190 0.1364 0.1613 REMARK 3 21 1.0500 - 1.0400 1.00 4107 222 0.1589 0.1521 REMARK 3 22 1.0400 - 1.0200 1.00 4074 219 0.1662 0.2020 REMARK 3 23 1.0200 - 1.0100 1.00 3999 220 0.1982 0.2300 REMARK 3 24 1.0100 - 0.9900 1.00 4114 211 0.2056 0.2342 REMARK 3 25 0.9900 - 0.9800 1.00 4017 235 0.2201 0.2176 REMARK 3 26 0.9800 - 0.9600 1.00 4063 200 0.2470 0.2712 REMARK 3 27 0.9600 - 0.9500 1.00 4079 198 0.2664 0.2854 REMARK 3 28 0.9500 - 0.9400 1.00 4059 205 0.2946 0.2968 REMARK 3 29 0.9400 - 0.9300 1.00 4101 203 0.3386 0.3376 REMARK 3 30 0.9300 - 0.9200 0.99 4037 187 0.3557 0.3700 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) : 0.094 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.883 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.86 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 : 0.013 814 REMARK 3 ANGLE : 1.291 1119 REMARK 3 CHIRALITY : 0.114 127 REMARK 3 PLANARITY : 0.011 151 REMARK 3 DIHEDRAL : 6.542 122 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 9GYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-19 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 : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7749 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 128152 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.920 REMARK 200 RESOLUTION RANGE LOW (A) : 39.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 1.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.800 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: BRIGHT 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, 2.6-3.6 M REMARK 280 AMMONIUM PHOSPHATE, VAPOR DIFFUSION, TEMPERATURE 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 15.15050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.66650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.66650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.15050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.70500 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 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 THR A 96 REMARK 465 ALA A 97 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 HOH A 238 O HOH A 292 2.05 REMARK 500 O HOH A 259 O HOH A 340 2.19 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 SER A 38 -69.60 -148.33 REMARK 500 SER A 38 -76.90 -144.38 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 120.0 REMARK 620 3 FES A 101 S2 99.2 101.9 REMARK 620 4 CYS A 44 SG 104.9 111.2 120.1 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 113.0 REMARK 620 3 FES A 101 S2 109.4 105.0 REMARK 620 4 CYS A 77 SG 108.3 118.4 101.9 REMARK 620 N 1 2 3 DBREF 9GYD A 1 97 UNP P00221 FER1_SPIOL 51 147 SEQADV 9GYD GLY A -7 UNP P00221 EXPRESSION TAG SEQADV 9GYD PRO A -6 UNP P00221 EXPRESSION TAG SEQADV 9GYD LEU A -5 UNP P00221 EXPRESSION TAG SEQADV 9GYD GLY A -4 UNP P00221 EXPRESSION TAG SEQADV 9GYD SER A -3 UNP P00221 EXPRESSION TAG SEQADV 9GYD PRO A -2 UNP P00221 EXPRESSION TAG SEQADV 9GYD GLU A -1 UNP P00221 EXPRESSION TAG SEQADV 9GYD PHE A 0 UNP P00221 EXPRESSION TAG 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 TYR 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 FES A 101 4 HETNAM FES FE2/S2 (INORGANIC) CLUSTER FORMUL 2 FES FE2 S2 FORMUL 3 HOH *147(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 GLY A 12 PRO A 19 0 SHEET 2 AA1 5 ALA A 2 THR A 9 -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 SG CYS A 39 FE1 FES A 101 1555 1555 2.33 LINK SG CYS A 44 FE1 FES A 101 1555 1555 2.30 LINK SG CYS A 47 FE2 FES A 101 1555 1555 2.30 LINK SG CYS A 77 FE2 FES A 101 1555 1555 2.30 CRYST1 30.301 51.410 61.333 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 0.033002 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016304 0.00000 CONECT 672 1533 CONECT 734 1533 CONECT 774 1534 CONECT 1252 1534 CONECT 1533 672 734 1535 1536 CONECT 1534 774 1252 1535 1536 CONECT 1535 1533 1534 CONECT 1536 1533 1534 MASTER 280 0 1 4 7 0 0 6 908 1 8 9 END