HEADER ELECTRON TRANSPORT 15-JAN-26 9TXE TITLE SPINACH FERREDOXIN I, OXIDISED 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 SPINACH FERREDOXIN, OXIDISED 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 REDOX, METALLOPROTEIN, IRON-SULFUR CLUSTER, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR S.LAXMI,S.B.CARR,K.A.VINCENT REVDAT 1 13-MAY-26 9TXE 0 JRNL AUTH S.LAXMI,S.JAHO,W.K.MYERS,K.A.VINCENT,S.B.CARR JRNL TITL CRYSTALLISE, POISE, CAPTURE: A MULTIMODAL PLATFORM FOR JRNL TITL 2 CORRELATED STRUCTURAL AND SPECTROSCOPIC CHARACTERISATION OF JRNL TITL 3 REDOX ENZYMES. JRNL REF J.BIOL.INORG.CHEM. 2026 JRNL REFN ESSN 1432-1327 JRNL PMID 42082801 JRNL DOI 10.1007/S00775-026-02148-X REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 59899 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1776 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 30.5800 - 2.2300 1.00 4813 140 0.1768 0.1902 REMARK 3 2 2.2300 - 1.7700 1.00 4611 139 0.1533 0.1551 REMARK 3 3 1.7700 - 1.5500 1.00 4560 146 0.1211 0.1466 REMARK 3 4 1.5500 - 1.4100 1.00 4545 141 0.1160 0.1353 REMARK 3 5 1.4100 - 1.3100 1.00 4507 141 0.1212 0.1646 REMARK 3 6 1.3100 - 1.2300 1.00 4505 142 0.1303 0.1484 REMARK 3 7 1.2300 - 1.1700 1.00 4486 136 0.1424 0.1682 REMARK 3 8 1.1700 - 1.1200 1.00 4504 109 0.1507 0.1530 REMARK 3 9 1.1200 - 1.0700 1.00 4490 156 0.1819 0.2086 REMARK 3 10 1.0700 - 1.0400 1.00 4440 145 0.2350 0.2476 REMARK 3 11 1.0400 - 1.0000 1.00 4461 139 0.3123 0.3213 REMARK 3 12 1.0000 - 0.9800 0.99 4444 139 0.3533 0.3634 REMARK 3 13 0.9800 - 0.9500 0.84 3757 103 0.3958 0.4007 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.135 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.028 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.35 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 : 0.006 800 REMARK 3 ANGLE : 0.898 1098 REMARK 3 CHIRALITY : 0.095 125 REMARK 3 PLANARITY : 0.006 148 REMARK 3 DIHEDRAL : 14.826 297 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 9TXE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-26. REMARK 100 THE DEPOSITION ID IS D_1292153632. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 - 7.9 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) : 0.7749 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 : 60723 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 39.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 1.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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 CUBES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 PHOSPHATE PH 7.8, 5% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 15.13250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.58450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.60600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.58450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.13250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.60600 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 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: 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 -71.23 -147.08 REMARK 500 SER A 38 -75.84 -144.62 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 120.3 REMARK 620 3 FES A 101 S2 100.2 102.6 REMARK 620 4 CYS A 44 SG 104.2 109.5 120.8 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 112.0 REMARK 620 3 FES A 101 S2 111.2 105.1 REMARK 620 4 CYS A 77 SG 108.1 117.2 102.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 29KI RELATED DB: PDB REMARK 900 RELATED ID: 9TXQ RELATED DB: PDB REMARK 900 RELATED ID: 9TXO RELATED DB: PDB DBREF 9TXE A 1 97 UNP P00221 FER1_SPIOL 51 147 SEQADV 9TXE GLY A -7 UNP P00221 EXPRESSION TAG SEQADV 9TXE PRO A -6 UNP P00221 EXPRESSION TAG SEQADV 9TXE LEU A -5 UNP P00221 EXPRESSION TAG SEQADV 9TXE GLY A -4 UNP P00221 EXPRESSION TAG SEQADV 9TXE SER A -3 UNP P00221 EXPRESSION TAG SEQADV 9TXE PRO A -2 UNP P00221 EXPRESSION TAG SEQADV 9TXE GLU A -1 UNP P00221 EXPRESSION TAG SEQADV 9TXE 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 *90(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 2.31 LINK SG CYS A 44 FE1 FES A 101 1555 1555 2.29 LINK SG CYS A 47 FE2 FES A 101 1555 1555 2.29 LINK SG CYS A 77 FE2 FES A 101 1555 1555 2.30 CRYST1 30.265 51.212 61.169 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 0.033041 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019527 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016348 0.00000 CONECT 342 779 CONECT 374 779 CONECT 395 780 CONECT 635 780 CONECT 779 342 374 781 782 CONECT 780 395 635 781 782 CONECT 781 779 780 CONECT 782 779 780 MASTER 260 0 1 4 7 0 0 6 851 1 8 9 END