HEADER OXIDOREDUCTASE 27-AUG-21 7RZB TITLE BRXA FROM STAPHYLOCOCCUS AUREUS WITH BACILLITHIOL MIXED DISULFIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACILLITHIOL SYSTEM OXIDOREDUCTASE, YPHP/YQIW FAMILY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRXA/BRXB FAMILY BACILLIREDOXIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: A2U18_07020, C7P97_04720, CSC83_09870, CSC87_03980, SOURCE 5 GF559_09020, HU771_05980, SAMEA70245418_01058; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BACILLITHIOL, REDOX, OXIDATIVE STRESS, BACILLIREDOXIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.D.COOK,C.S.MCHUGH REVDAT 2 18-OCT-23 7RZB 1 REMARK REVDAT 1 13-APR-22 7RZB 0 JRNL AUTH C.S.MCHUGH,P.D.COOK JRNL TITL STRUCTURE OF BRXA FROM STAPHYLOCOCCUS AUREUS, A JRNL TITL 2 BACILLIREDOXIN INVOLVED IN REDOX HOMEOSTASIS IN FIRMICUTES. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 78 144 2022 JRNL REFN ESSN 2053-230X REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20234 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1044 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 33.8760 - 3.0594 1.00 2945 148 0.1779 0.1921 REMARK 3 2 3.0594 - 2.4286 1.00 2771 145 0.2067 0.2143 REMARK 3 3 2.4286 - 2.1216 1.00 2745 164 0.2026 0.2434 REMARK 3 4 2.1216 - 1.9277 1.00 2708 155 0.2025 0.2668 REMARK 3 5 1.9277 - 1.7895 1.00 2684 161 0.2195 0.2870 REMARK 3 6 1.7895 - 1.6840 0.99 2713 139 0.2322 0.3013 REMARK 3 7 1.6840 - 1.6000 0.97 2624 132 0.2776 0.3319 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.640 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.16 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 1118 REMARK 3 ANGLE : 0.861 1524 REMARK 3 CHIRALITY : 0.056 175 REMARK 3 PLANARITY : 0.004 207 REMARK 3 DIHEDRAL : 6.820 908 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 7RZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-21. REMARK 100 THE DEPOSITION ID IS D_1000259292. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20331 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 60.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04300 REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.58900 REMARK 200 R SYM FOR SHELL (I) : 0.58900 REMARK 200 FOR SHELL : 1.300 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: PDB ENTRY 3FHK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM AMMONIUM PHOSPHATE, 10% W/V REMARK 280 PEG3350, 10 MM HEPES, 25 MM SODIUM CHLORIDE, 18 MG/ML BRXA, 1 MM REMARK 280 BACILLITHIOL DISULFIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 20.51850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.44100 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.44100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.25925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.44100 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.44100 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.77775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.44100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.44100 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 10.25925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.44100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.44100 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.77775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 20.51850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 P PO4 A 202 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 388 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 389 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 413 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 TYR A 4 REMARK 465 ASP A 5 REMARK 465 ALA A 6 REMARK 465 TYR A 7 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 8 CG SD CE REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 GLU A 10 CG CD OE1 OE2 REMARK 470 GLU A 73 CG CD OE1 OE2 REMARK 470 LYS A 145 CG CD CE NZ 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 422 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 423 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A 424 DISTANCE = 7.62 ANGSTROMS DBREF1 7RZB A 1 145 UNP A0A229LVN5_STAAU DBREF2 7RZB A A0A229LVN5 1 145 SEQADV 7RZB GLY A -1 UNP A0A229LVN EXPRESSION TAG SEQADV 7RZB HIS A 0 UNP A0A229LVN EXPRESSION TAG SEQRES 1 A 147 GLY HIS MET ASN ALA TYR ASP ALA TYR MET LYS GLU ILE SEQRES 2 A 147 ALA GLN GLN MET ARG GLY GLU LEU THR GLN ASN GLY PHE SEQRES 3 A 147 THR SER LEU GLU THR SER GLU ALA VAL SER GLU TYR MET SEQRES 4 A 147 ASN GLN VAL ASN ALA ASP ASP THR THR PHE VAL VAL ILE SEQRES 5 A 147 ASN SER THR CYS GLY CYS ALA ALA GLY LEU ALA ARG PRO SEQRES 6 A 147 ALA ALA VAL ALA VAL ALA THR GLN ASN GLU HIS ARG PRO SEQRES 7 A 147 THR ASN THR VAL THR VAL PHE ALA GLY GLN ASP LYS GLU SEQRES 8 A 147 ALA THR ALA THR MET ARG GLU PHE ILE GLN GLN VAL PRO SEQRES 9 A 147 SER SER PRO SER TYR ALA LEU PHE LYS GLY ARG ASP LEU SEQRES 10 A 147 VAL TYR PHE MET PRO ARG GLU PHE ILE GLU GLY ARG ASP SEQRES 11 A 147 ILE ASN ASP ILE ALA MET ASP LEU LYS ASP ALA PHE ASP SEQRES 12 A 147 GLU ASN CYS LYS HET G5M A 201 26 HET PO4 A 202 5 HETNAM G5M (2S)-2-{[2-(L-CYSTEINYLAMINO)-2-DEOXY-ALPHA-D- HETNAM 2 G5M GLUCOPYRANOSYL]OXY}BUTANEDIOIC ACID HETNAM PO4 PHOSPHATE ION FORMUL 2 G5M C13 H22 N2 O10 S FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *124(H2 O) HELIX 1 AA1 MET A 8 GLN A 21 1 14 HELIX 2 AA2 THR A 29 ASN A 38 1 10 HELIX 3 AA3 CYS A 54 ASN A 72 1 19 HELIX 4 AA4 ASP A 87 GLN A 99 1 13 HELIX 5 AA5 PRO A 120 ILE A 124 5 5 HELIX 6 AA6 ASP A 128 CYS A 144 1 17 SHEET 1 AA1 5 THR A 25 SER A 26 0 SHEET 2 AA1 5 ASN A 78 PHE A 83 1 O THR A 79 N THR A 25 SHEET 3 AA1 5 THR A 45 ASN A 51 1 N ASN A 51 O VAL A 82 SHEET 4 AA1 5 SER A 106 LYS A 111 -1 O ALA A 108 N VAL A 48 SHEET 5 AA1 5 ASP A 114 MET A 119 -1 O VAL A 116 N LEU A 109 SSBOND 1 CYS A 56 CYS A 56 1555 7555 2.93 LINK SG CYS A 54 S26 G5M A 201 1555 1555 2.02 CISPEP 1 SER A 104 PRO A 105 0 -6.17 CRYST1 84.882 84.882 41.037 90.00 90.00 90.00 P 41 21 2 8 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 0.011781 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024368 0.00000