HEADER DNA BINDING PROTEIN 18-JUL-25 9VXG TITLE ROS-SENSING TRANSCRIPTION FACTOR YCHJ REGULATES THE RSSB-RPOS PATHWAY TITLE 2 TO PROTECT SALMONELLA AGAINST OXIDATIVE ATTACK BY MACROPHAGES COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0225 PROTEIN YCHJ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: UPF0225 PROTEIN YCHJ; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM STR. 14028S; SOURCE 4 ORGANISM_TAXID: 588858; SOURCE 5 GENE: YCHJ, STM1755; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 10 TYPHIMURIUM STR. 14028S; SOURCE 11 ORGANISM_TAXID: 588858; SOURCE 12 GENE: YCHJ, STM1755; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DNA BINDING, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.L.YUAN,W.W.WANG REVDAT 1 06-AUG-25 9VXG 0 JRNL AUTH W.W.WANG,X.L.YUAN JRNL TITL ROS-SENSING TRANSCRIPTION FACTOR YCHJ REGULATES THE JRNL TITL 2 RSSB-RPOS PATHWAY TO PROTECT SALMONELLA AGAINST OXIDATIVE JRNL TITL 3 ATTACK BY MACROPHAGES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.1_3469: ???) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 505 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 29.4680 - 3.6521 1.00 2589 124 0.1960 0.2225 REMARK 3 2 3.6521 - 2.8996 1.00 2463 107 0.2685 0.3350 REMARK 3 3 2.8996 - 2.5333 1.00 2386 139 0.3060 0.3190 REMARK 3 4 2.5333 - 2.3020 1.00 2351 135 0.2762 0.3162 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.12 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 : 0.005 1202 REMARK 3 ANGLE : 0.789 1620 REMARK 3 CHIRALITY : 0.051 161 REMARK 3 PLANARITY : 0.005 212 REMARK 3 DIHEDRAL : 3.155 712 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 9VXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 23-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10353 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 53.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 20.00 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 (%): 62.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M AMMONIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PROPANE PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 62.18350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.46850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.46850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 93.27525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.46850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.46850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 31.09175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.46850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.46850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 93.27525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.46850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.46850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 31.09175 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 62.18350 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 SG CYS A 17 ZN ZN A 201 1.63 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 CYS A 16 -105.58 -119.50 REMARK 500 ALA A 46 -46.00 75.44 REMARK 500 ILE A 125 -52.05 -139.74 REMARK 500 PRO B 137 98.63 -44.30 REMARK 500 CYS B 138 112.78 -38.13 REMARK 500 PRO B 139 -9.78 -58.29 REMARK 500 LYS B 144 -92.67 -135.92 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 7 SG 104.0 REMARK 620 3 CYS A 16 SG 109.2 102.8 REMARK 620 N 1 2 DBREF 9VXG A 1 130 UNP Q8ZP43 YCHJ_SALTY 1 130 DBREF 9VXG B 133 148 UNP Q8ZP43 YCHJ_SALTY 133 148 SEQADV 9VXG LYS A 0 UNP Q8ZP43 EXPRESSION TAG SEQRES 1 A 131 LYS MET SER GLN PRO CYS PRO CYS GLY SER ALA ASP GLU SEQRES 2 A 131 TYR SER LEU CYS CYS GLY ARG ILE VAL SER GLY GLU ARG SEQRES 3 A 131 VAL ALA PRO ASP PRO SER HIS LEU MET ARG SER ARG TYR SEQRES 4 A 131 CYS ALA PHE VAL MET LYS ASP ALA ASP TYR LEU ILE LYS SEQRES 5 A 131 SER TRP HIS PRO THR CYS ASN ALA ALA ALA PHE ARG ASP SEQRES 6 A 131 ASP ILE ILE ALA GLY PHE ALA ASN THR ARG TRP LEU GLY SEQRES 7 A 131 LEU THR ILE PHE GLU HIS THR TRP SER GLU ALA GLU ASN SEQRES 8 A 131 THR GLY TYR VAL SER PHE ILE ALA ARG PHE SER GLU GLN SEQRES 9 A 131 GLY LYS ASN GLY ALA ILE ILE GLU ARG SER ARG PHE ILE SEQRES 10 A 131 LYS GLU ASN GLY GLN TRP TYR TYR ILE ASP GLY THR ARG SEQRES 11 A 131 PRO SEQRES 1 B 16 GLY ARG ASN ASP PRO CYS PRO CYS GLY SER GLY LYS LYS SEQRES 2 B 16 PHE LYS LYS HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *20(H2 O) HELIX 1 AA1 GLU A 12 CYS A 16 5 5 HELIX 2 AA2 CYS A 17 SER A 22 1 6 HELIX 3 AA3 ASP A 29 MET A 43 1 15 HELIX 4 AA4 ALA A 46 SER A 52 1 7 HELIX 5 AA5 HIS A 54 ALA A 61 5 8 HELIX 6 AA6 PHE A 62 ALA A 71 1 10 SHEET 1 AA1 4 ARG A 74 SER A 86 0 SHEET 2 AA1 4 THR A 91 GLU A 102 -1 O TYR A 93 N THR A 84 SHEET 3 AA1 4 LYS A 105 GLU A 118 -1 O LYS A 105 N GLU A 102 SHEET 4 AA1 4 GLN A 121 THR A 128 -1 O ASP A 126 N ARG A 114 SSBOND 1 CYS B 138 CYS B 140 1555 1555 2.05 LINK SG CYS A 5 ZN ZN A 201 1555 1555 2.28 LINK SG CYS A 7 ZN ZN A 201 1555 1555 1.97 LINK SG CYS A 16 ZN ZN A 201 1555 1555 2.22 CRYST1 58.937 58.937 124.367 90.00 90.00 90.00 P 43 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 0.016967 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016967 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008041 0.00000 CONECT 45 1164 CONECT 58 1164 CONECT 122 1164 CONECT 1088 1101 CONECT 1101 1088 CONECT 1164 45 58 122 MASTER 252 0 1 6 4 0 0 6 1182 2 6 13 END