HEADER OXIDOREDUCTASE 29-SEP-24 9GXC TITLE ROOM TEMPERATURE STRUCTURE OF FAD-CONTAINING FERRODOXIN-NADP REDUCTASE TITLE 2 FROM BRUCELLA OVIS AT LCLS 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 1 27-NOV-24 9GXC 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. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 48.250 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13025 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 628 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 35.2000 - 3.4900 0.95 3113 166 0.1289 0.1419 REMARK 3 2 3.4900 - 2.7700 0.95 3106 156 0.2060 0.2642 REMARK 3 3 2.7700 - 2.4200 0.96 3125 133 0.2774 0.3183 REMARK 3 4 2.4200 - 2.2000 0.95 3053 173 0.7283 0.7729 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) : 22.930 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 : 0.002 NULL REMARK 3 ANGLE : 0.498 NULL REMARK 3 CHIRALITY : 0.041 320 REMARK 3 PLANARITY : 0.005 373 REMARK 3 DIHEDRAL : 8.890 282 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 9GXC 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_1292141326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-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 : MFX REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE MFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.107 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : SLAC EPIX10K 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL 0.10.2 REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 35.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 413.0 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 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 FOR SHELL : 0.200 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 83.80000 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 41.90000 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 125.70000 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: 1260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 465 FAD A 259 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 OE1 GLU A 66 O HOH A 401 1.95 REMARK 500 OE1 GLU A 252 O HOH A 402 2.17 REMARK 500 O ARG A 135 O HOH A 403 2.17 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 -15.70 71.18 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9GXC A 1 258 UNP A0A0H3ASL8_BRUO2 DBREF2 9GXC A A0A0H3ASL8 1 258 SEQADV 9GXC GLY A -4 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXC PRO A -3 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXC GLY A -2 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXC SER A -1 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXC HIS A 0 UNP A0A0H3ASL EXPRESSION TAG SEQADV 9GXC FAD A 259 UNP A0A0H3ASL EXPRESSION TAG SEQRES 1 A 264 GLY PRO GLY SER HIS MET SER SER ASN PHE ASN GLN GLU SEQRES 2 A 264 THR VAL THR ASP ILE HIS HIS TRP THR ASP THR LEU PHE SEQRES 3 A 264 SER PHE ARG THR THR ARG ASP PRO GLY PHE ARG PHE GLN SEQRES 4 A 264 SER GLY GLN PHE ILE MET MET GLY LEU GLU VAL ASN GLY SEQRES 5 A 264 LYS PRO LEU THR ARG ALA TYR SER ILE ALA SER SER LEU SEQRES 6 A 264 TYR GLU ASP GLY LEU GLU PHE PHE SER ILE LYS VAL PRO SEQRES 7 A 264 ASN GLY PRO LEU THR SER LYS LEU GLN HIS LEU LYS LYS SEQRES 8 A 264 GLY ASP GLN ILE ILE VAL SER LYS LYS PRO VAL GLY THR SEQRES 9 A 264 LEU LEU TYR ASP ASN LEU LYS PRO GLY LYS HIS LEU TRP SEQRES 10 A 264 LEU LEU SER THR GLY THR GLY LEU ALA PRO PHE LEU SER SEQRES 11 A 264 ILE ILE ARG ASP LEU GLU VAL TYR GLU ARG PHE GLU LYS SEQRES 12 A 264 VAL ILE LEU VAL HIS GLY VAL ARG GLN VAL ALA GLU LEU SEQRES 13 A 264 ALA TYR THR ASP PHE ILE SER ASN GLU LEU PRO GLN ASP SEQRES 14 A 264 GLU PHE LEU GLY GLU MET VAL LYS ASN GLN LEU ILE TYR SEQRES 15 A 264 TYR PRO THR VAL THR ARG GLU PRO TYR LYS THR ARG GLY SEQRES 16 A 264 ARG LEU THR ASP LEU ILE ARG SER GLY GLN LEU PHE LYS SEQRES 17 A 264 ASP VAL GLY LEU PRO GLU PHE ASN HIS GLU ASP ASP ARG SEQRES 18 A 264 MET MET LEU CYS GLY SER PRO GLU MET LEU ALA GLU THR SEQRES 19 A 264 LYS GLN ILE LEU GLU GLU ARG GLY PHE THR GLU GLY SER SEQRES 20 A 264 GLN SER GLU PRO GLY GLU PHE VAL ILE GLU LYS ALA PHE SEQRES 21 A 264 VAL GLU LYS FAD HET FAD A 301 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *23(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 GLU A 160 1 8 HELIX 7 AA7 LEU A 167 GLN A 174 1 8 HELIX 8 AA8 ARG A 191 SER A 198 1 8 HELIX 9 AA9 GLY A 199 GLY A 206 1 8 HELIX 10 AB1 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 MET A 41 O ARG A 52 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 SER A 69 N PHE A 21 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 VAL A 142 SHEET 4 AA2 5 ASP A 215 GLY A 221 1 O ARG A 216 N TRP A 112 SHEET 5 AA2 5 PHE A 249 LYS A 253 1 O GLU A 252 N LEU A 219 CRYST1 39.600 39.600 167.600 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 0.025253 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005967 0.00000