HEADER OXIDOREDUCTASE 29-SEP-24 9GXB TITLE ROOM TEMPERATURE STRUCTURE OF FAD-CONTAINING FERRODOXIN-NADP REDUCTASE TITLE 2 FROM BRUCELLA OVIS AT EUXFEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: FERREDOXIN--NADP(+) REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.18.1.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA OVIS ATCC 25840; SOURCE 3 ORGANISM_TAXID: 444178; SOURCE 4 GENE: FPR, BOV_0348; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FERREDOXIN-NADP+ REDUCTASE, ROOM TEMPERATURE X-RAY DIFFRACTION, KEYWDS 2 ELECTRON TRANSFER, OXIDATIVE DAMAGE PROTECTION, SERIAL FEMTOSECOND KEYWDS 3 CRYSTALLOGRAPHY, XFEL, MICROCRYSTALS., OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MARTINEZ-JULVEZ,J.M.MARTIN-GARCIA,M.MEDINA REVDAT 2 25-DEC-24 9GXB 1 REMARK REVDAT 1 27-NOV-24 9GXB 0 JRNL AUTH A.MORENO,I.QUEREDA-MORALEDA,C.LOZANO-VALLHONRAT, JRNL AUTH 2 M.BUNUEL-ESCUDERO,S.BOTHA,C.KUPITZ,S.LISOVA,R.SIERRA, JRNL AUTH 3 V.MARIANI,P.SCHLEISSNER,L.B.GEE,K.DORNER,C.SCHMIDT,H.HAN, JRNL AUTH 4 M.KLOOS,P.SMYTH,J.VALERIO,J.SCHULZ,R.DE WIJN,D.V.M.MELO, JRNL AUTH 5 A.ROUND,F.TROST,E.SOBOLEV,E.JUNCHENG,M.SIKORSKI,R.BEAN, JRNL AUTH 6 M.MARTINEZ-JULVEZ,J.M.MARTIN-GARCIA,M.MEDINA JRNL TITL NEW INSIGHTS INTO THE FUNCTION AND MOLECULAR MECHANISMS OF JRNL TITL 2 FERREDOXIN-NADP + REDUCTASE FROM BRUCELLA OVIS. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 762 10204 2024 JRNL REFN ESSN 1096-0384 JRNL PMID 39522858 JRNL DOI 10.1016/J.ABB.2024.110204 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1039 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 22.9700 - 3.6300 0.95 2805 158 0.1713 0.2005 REMARK 3 2 3.6300 - 2.8800 0.96 2824 129 0.2115 0.2533 REMARK 3 3 2.8800 - 2.5200 0.95 2830 135 0.2348 0.2625 REMARK 3 4 2.5200 - 2.2900 0.94 2763 169 0.2490 0.2822 REMARK 3 5 2.2900 - 2.1300 0.96 2814 131 0.2613 0.2977 REMARK 3 6 2.1300 - 2.0000 0.95 2788 155 0.2915 0.3051 REMARK 3 7 2.0000 - 1.9000 0.94 2747 162 0.3679 0.4406 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 NULL REMARK 3 ANGLE : 0.704 NULL REMARK 3 CHIRALITY : 0.045 320 REMARK 3 PLANARITY : 0.006 373 REMARK 3 DIHEDRAL : 8.929 282 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 9GXB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292141327. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : SPB/SFX REMARK 200 X-RAY GENERATOR MODEL : EUROPEAN XFEL BEAMLINE SPB/SFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.319 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : AGIPD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20670 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 23.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 48.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4.000 0.1M MES PH 6.5 0.2M REMARK 280 MGCL2, BATCH MODE, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 84.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.12500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 126.37500 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: 1270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 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 -4 REMARK 465 PRO A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 OE2 GLU A 252 O HOH A 401 2.07 REMARK 500 O HOH A 440 O HOH A 450 2.13 REMARK 500 O SER A 3 O HOH A 402 2.18 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 3 -7.56 71.70 REMARK 500 THR A 17 -163.88 -124.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 464 DISTANCE = 6.52 ANGSTROMS DBREF1 9GXB A 1 258 UNP A0A0H3ASL8_BRUO2 DBREF2 9GXB A A0A0H3ASL8 1 258 SEQADV 9GXB GLY A -4 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXB PRO A -3 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXB GLY A -2 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXB SER A -1 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXB HIS A 0 UNP A0A0H3ASL EXPRESSION TAG SEQRES 1 A 263 GLY PRO GLY SER HIS MET SER SER ASN PHE ASN GLN GLU SEQRES 2 A 263 THR VAL THR ASP ILE HIS HIS TRP THR ASP THR LEU PHE SEQRES 3 A 263 SER PHE ARG THR THR ARG ASP PRO GLY PHE ARG PHE GLN SEQRES 4 A 263 SER GLY GLN PHE ILE MET MET GLY LEU GLU VAL ASN GLY SEQRES 5 A 263 LYS PRO LEU THR ARG ALA TYR SER ILE ALA SER SER LEU SEQRES 6 A 263 TYR GLU ASP GLY LEU GLU PHE PHE SER ILE LYS VAL PRO SEQRES 7 A 263 ASN GLY PRO LEU THR SER LYS LEU GLN HIS LEU LYS LYS SEQRES 8 A 263 GLY ASP GLN ILE ILE VAL SER LYS LYS PRO VAL GLY THR SEQRES 9 A 263 LEU LEU TYR ASP ASN LEU LYS PRO GLY LYS HIS LEU TRP SEQRES 10 A 263 LEU LEU SER THR GLY THR GLY LEU ALA PRO PHE LEU SER SEQRES 11 A 263 ILE ILE ARG ASP LEU GLU VAL TYR GLU ARG PHE GLU LYS SEQRES 12 A 263 VAL ILE LEU VAL HIS GLY VAL ARG GLN VAL ALA GLU LEU SEQRES 13 A 263 ALA TYR THR ASP PHE ILE SER ASN GLU LEU PRO GLN ASP SEQRES 14 A 263 GLU PHE LEU GLY GLU MET VAL LYS ASN GLN LEU ILE TYR SEQRES 15 A 263 TYR PRO THR VAL THR ARG GLU PRO TYR LYS THR ARG GLY SEQRES 16 A 263 ARG LEU THR ASP LEU ILE ARG SER GLY GLN LEU PHE LYS SEQRES 17 A 263 ASP VAL GLY LEU PRO GLU PHE ASN HIS GLU ASP ASP ARG SEQRES 18 A 263 MET MET LEU CYS GLY SER PRO GLU MET LEU ALA GLU THR SEQRES 19 A 263 LYS GLN ILE LEU GLU GLU ARG GLY PHE THR GLU GLY SER SEQRES 20 A 263 GLN SER GLU PRO GLY GLU PHE VAL ILE GLU LYS ALA PHE SEQRES 21 A 263 VAL GLU LYS HET FAD A 301 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *64(H2 O) HELIX 1 AA1 LEU A 77 GLN A 82 1 6 HELIX 2 AA2 LEU A 101 LEU A 105 5 5 HELIX 3 AA3 LEU A 120 ILE A 127 1 8 HELIX 4 AA4 ASP A 129 PHE A 136 1 8 HELIX 5 AA5 GLN A 147 LEU A 151 5 5 HELIX 6 AA6 TYR A 153 ASN A 159 1 7 HELIX 7 AA7 GLU A 160 ASP A 164 5 5 HELIX 8 AA8 LEU A 167 GLN A 174 1 8 HELIX 9 AA9 ARG A 191 SER A 198 1 8 HELIX 10 AB1 GLY A 199 GLY A 206 1 8 HELIX 11 AB2 SER A 222 ARG A 236 1 15 SHEET 1 AA1 6 LYS A 48 SER A 55 0 SHEET 2 AA1 6 PHE A 38 VAL A 45 -1 N LEU A 43 O LEU A 50 SHEET 3 AA1 6 GLN A 89 SER A 93 -1 O SER A 93 N MET A 40 SHEET 4 AA1 6 PHE A 5 HIS A 15 -1 N ASN A 6 O VAL A 92 SHEET 5 AA1 6 LEU A 20 THR A 25 -1 O SER A 22 N HIS A 14 SHEET 6 AA1 6 LEU A 65 ILE A 70 -1 O LEU A 65 N THR A 25 SHEET 1 AA2 5 LEU A 175 VAL A 181 0 SHEET 2 AA2 5 LYS A 138 VAL A 145 1 N LEU A 141 O ILE A 176 SHEET 3 AA2 5 HIS A 110 THR A 116 1 N LEU A 113 O ILE A 140 SHEET 4 AA2 5 ASP A 215 GLY A 221 1 O MET A 218 N TRP A 112 SHEET 5 AA2 5 PHE A 249 LYS A 253 1 O VAL A 250 N LEU A 219 CRYST1 39.900 39.900 168.500 90.00 90.00 90.00 P 41 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 0.025063 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005935 0.00000