HEADER ELECTRON TRANSPORT 01-SEP-25 9Y2G TITLE RUBREDOXIN FROM PYROCOCCUS FURIOSUS AT 293K, FORMYL-METHIONINE N- TITLE 2 TERMINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RUBREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RD; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 2261; SOURCE 4 GENE: RUB, PF1282; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE E20; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 3003230; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IRON-SULFUR PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.DOUKOV,S.P.J.CRAMER,D.GEORGE,F.E.JENNEY REVDAT 1 29-APR-26 9Y2G 0 JRNL AUTH T.DOUKOV,I.LEONTYEV,F.E.JENNEY JR.,D.GEORGE,S.P.CRAMER JRNL TITL SOME LIKE IT HOT -STRUCTURAL CHANGES IN EXTREMOPHILE JRNL TITL 2 RUBREDOXIN AT 120 °C. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 65 20302 2026 JRNL REFN ESSN 1521-3773 JRNL PMID 41287388 JRNL DOI 10.1002/ANIE.202520302 REMARK 2 REMARK 2 RESOLUTION. 1.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 73.9 REMARK 3 NUMBER OF REFLECTIONS : 13728 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.138 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 695 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.14 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 1.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 1 REMARK 3 BIN FREE R VALUE : 0.0760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 423 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : 0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.485 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.969 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 435 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 380 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 587 ; 1.845 ; 1.806 REMARK 3 BOND ANGLES OTHERS (DEGREES): 897 ; 0.631 ; 1.785 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 52 ; 6.225 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1 ; 4.516 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 67 ;10.083 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 58 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 499 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 81 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 215 ; 6.041 ; 1.956 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 215 ; 5.883 ; 1.951 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 264 ; 8.330 ; 4.364 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 265 ; 8.358 ; 4.394 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 220 ;12.357 ; 2.966 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 219 ;11.847 ; 2.916 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 324 ;16.756 ; 6.255 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 480 ;19.728 ;17.030 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 475 ;19.534 ;16.350 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 815 ; 4.471 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 54 REMARK 3 RESIDUE RANGE : A 101 A 101 REMARK 3 ORIGIN FOR THE GROUP (A): 13.287 -1.927 -4.422 REMARK 3 T TENSOR REMARK 3 T11: 0.0217 T22: 0.0043 REMARK 3 T33: 0.0239 T12: -0.0056 REMARK 3 T13: -0.0074 T23: 0.0052 REMARK 3 L TENSOR REMARK 3 L11: 3.8213 L22: 4.9458 REMARK 3 L33: 2.5164 L12: 1.8380 REMARK 3 L13: -0.7511 L23: -1.2603 REMARK 3 S TENSOR REMARK 3 S11: 0.0340 S12: -0.0120 S13: 0.2416 REMARK 3 S21: 0.1096 S22: -0.1008 S23: -0.0169 REMARK 3 S31: -0.2245 S32: 0.0726 S33: 0.0667 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9Y2G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-SEP-25. REMARK 100 THE DEPOSITION ID IS D_1000299736. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-25 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14424 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.140 REMARK 200 RESOLUTION RANGE LOW (A) : 27.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.14 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.23800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION AGAINST 3.1 M NACL REMARK 280 WITH 3.6M NA,K PHOSPHATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 17.06650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.86250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.34350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.86250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.06650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.34350 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 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 CYS A 9 SG 112.4 REMARK 620 3 CYS A 39 SG 114.0 101.9 REMARK 620 4 CYS A 42 SG 102.3 115.0 111.6 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9XZU RELATED DB: PDB REMARK 900 100K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y00 RELATED DB: PDB REMARK 900 140K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y0Y RELATED DB: PDB REMARK 900 180K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y0Z RELATED DB: PDB REMARK 900 200K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y11 RELATED DB: PDB REMARK 900 220K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y1U RELATED DB: PDB REMARK 900 240K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y28 RELATED DB: PDB REMARK 900 260K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y29 RELATED DB: PDB REMARK 900 280K ALANINE N-TERMINUS REMARK 900 RELATED ID: 9Y2E RELATED DB: PDB REMARK 900 100K FORMYL METHIONINE N-TERMINUS DBREF 9Y2G A 1 54 UNP P24297 RUBR_PYRFU 1 54 SEQRES 1 A 54 FME ALA LYS TRP VAL CYS LYS ILE CYS GLY TYR ILE TYR SEQRES 2 A 54 ASP GLU ASP ALA GLY ASP PRO ASP ASN GLY ILE SER PRO SEQRES 3 A 54 GLY THR LYS PHE GLU GLU LEU PRO ASP ASP TRP VAL CYS SEQRES 4 A 54 PRO ILE CYS GLY ALA PRO LYS SER GLU PHE GLU LYS LEU SEQRES 5 A 54 GLU ASP MODRES 9Y2G FME A 1 MET MODIFIED RESIDUE HET FME A 1 10 HET ZN A 101 1 HETNAM FME N-FORMYLMETHIONINE HETNAM ZN ZINC ION FORMUL 1 FME C6 H11 N O3 S FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *51(H2 O) HELIX 1 AA1 ASP A 19 GLY A 23 5 5 HELIX 2 AA2 LYS A 29 LEU A 33 5 5 HELIX 3 AA3 PRO A 45 SER A 47 5 3 SHEET 1 AA1 3 ILE A 12 ASP A 14 0 SHEET 2 AA1 3 LYS A 3 CYS A 6 -1 N TRP A 4 O TYR A 13 SHEET 3 AA1 3 PHE A 49 LYS A 51 -1 O GLU A 50 N VAL A 5 LINK C FME A 1 N ALA A 2 1555 1555 1.40 LINK SG CYS A 6 ZN ZN A 101 1555 1555 2.35 LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.32 LINK SG CYS A 39 ZN ZN A 101 1555 1555 2.35 LINK SG CYS A 42 ZN ZN A 101 1555 1555 2.34 CRYST1 34.133 34.687 43.725 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 0.029297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028829 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022870 0.00000 CONECT 1 2 4 CONECT 2 1 3 CONECT 3 2 CONECT 4 1 5 9 CONECT 5 4 6 CONECT 6 5 7 CONECT 7 6 8 CONECT 8 7 CONECT 9 4 10 11 CONECT 10 9 CONECT 11 9 CONECT 51 425 CONECT 74 425 CONECT 307 425 CONECT 328 425 CONECT 425 51 74 307 328 MASTER 287 0 2 3 3 0 0 6 475 1 16 5 END