HEADER ELECTRON TRANSPORT 17-MAR-26 29KI TITLE SPINACH FERREDOXIN I, REDUCED, -400 MV 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, REDUCED, -400 MV 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 29KI 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. 1.11 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 38111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1833 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 30.5500 - 2.6100 1.00 3007 143 0.1780 0.2115 REMARK 3 2 2.6100 - 2.0700 1.00 2870 132 0.1614 0.1884 REMARK 3 3 2.0700 - 1.8100 1.00 2833 138 0.1404 0.1626 REMARK 3 4 1.8100 - 1.6400 1.00 2780 159 0.1202 0.1355 REMARK 3 5 1.6400 - 1.5300 1.00 2798 134 0.1195 0.1671 REMARK 3 6 1.5300 - 1.4400 1.00 2801 136 0.1273 0.1506 REMARK 3 7 1.4400 - 1.3600 1.00 2763 132 0.1444 0.1801 REMARK 3 8 1.3600 - 1.3100 1.00 2754 169 0.1629 0.2141 REMARK 3 9 1.3000 - 1.2500 1.00 2755 139 0.1921 0.2278 REMARK 3 10 1.2500 - 1.2100 1.00 2747 165 0.2138 0.2257 REMARK 3 11 1.2100 - 1.1700 1.00 2744 145 0.2398 0.2764 REMARK 3 12 1.1700 - 1.1400 0.99 2754 130 0.2831 0.3078 REMARK 3 13 1.1400 - 1.1100 0.93 2557 111 0.3357 0.3366 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) : 0.117 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.538 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.71 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 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 : 0.009 800 REMARK 3 ANGLE : 1.024 1098 REMARK 3 CHIRALITY : 0.095 125 REMARK 3 PLANARITY : 0.008 148 REMARK 3 DIHEDRAL : 16.032 297 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 29KI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1292155302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-26 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) : 0.6199 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 : 470734 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 30.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 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 (%): 42.75 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, BATCH MODE, 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 15.01000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.54500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.54500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.01000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.77500 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 -70.71 -149.61 REMARK 500 SER A 38 -75.79 -146.89 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 120.1 REMARK 620 3 FES A 101 S2 101.3 101.9 REMARK 620 4 CYS A 44 SG 104.0 109.4 121.0 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 112.3 REMARK 620 3 FES A 101 S2 111.3 105.2 REMARK 620 4 CYS A 77 SG 107.7 117.0 103.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9TXQ RELATED DB: PDB REMARK 900 RELATED ID: 9TXO RELATED DB: PDB REMARK 900 RELATED ID: 9TXE RELATED DB: PDB DBREF 29KI A 1 97 UNP P00221 FER1_SPIOL 51 147 SEQADV 29KI GLY A -7 UNP P00221 EXPRESSION TAG SEQADV 29KI PRO A -6 UNP P00221 EXPRESSION TAG SEQADV 29KI LEU A -5 UNP P00221 EXPRESSION TAG SEQADV 29KI GLY A -4 UNP P00221 EXPRESSION TAG SEQADV 29KI SER A -3 UNP P00221 EXPRESSION TAG SEQADV 29KI PRO A -2 UNP P00221 EXPRESSION TAG SEQADV 29KI GLU A -1 UNP P00221 EXPRESSION TAG SEQADV 29KI 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 *77(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 2.30 LINK SG CYS A 44 FE1 FES A 101 1555 1555 2.27 LINK SG CYS A 47 FE2 FES A 101 1555 1555 2.28 LINK SG CYS A 77 FE2 FES A 101 1555 1555 2.30 CRYST1 30.020 51.550 61.090 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 0.033311 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016369 0.00000 CONECT 653 1502 CONECT 715 1502 CONECT 755 1503 CONECT 1221 1503 CONECT 1502 653 715 1504 1505 CONECT 1503 755 1221 1504 1505 CONECT 1504 1502 1503 CONECT 1505 1502 1503 MASTER 259 0 1 4 7 0 0 6 838 1 8 9 END