HEADER GENE REGULATION 20-AUG-25 9WEX TITLE CRYSTAL STRUCTURE OF PAS DOMAIN IN NREB PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR HISTIDINE KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.13.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LICHENIFORMIS; SOURCE 3 ORGANISM_TAXID: 1402; SOURCE 4 GENE: CHCC16736_1389, I6G80_11755; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 2FE-2S CLUSTER;SULFIDE SENSOR;HISTIDINE PROTEIN KINASE; TWO-COMPONENT KEYWDS 2 SYSTEM NREBC., GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIA,L.XUN,C.TANG REVDAT 1 03-JUN-26 9WEX 0 JRNL AUTH C.TANG JRNL TITL A THREE-CYSTEINE COORDINATED 2FE-2S CLUSTER MEDIATES JRNL TITL 2 SPECIFIC H2S SENSING THROUGH PERSULFIDATION AND SULFENATION JRNL TITL 3 IN BACTERIAL HISTIDINE KINASE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20526 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1015 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 25.2100 - 2.9100 1.00 2997 145 0.1504 0.1950 REMARK 3 2 2.9100 - 2.3100 1.00 2777 172 0.1674 0.1890 REMARK 3 3 2.3100 - 2.0200 1.00 2753 167 0.1509 0.1880 REMARK 3 4 2.0200 - 1.8300 1.00 2766 132 0.1350 0.1889 REMARK 3 5 1.8300 - 1.7000 1.00 2751 131 0.1368 0.1933 REMARK 3 6 1.7000 - 1.6000 1.00 2726 155 0.1394 0.2007 REMARK 3 7 1.6000 - 1.5200 1.00 2741 113 0.2009 0.2320 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) : 0.162 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.692 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.75 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 1007 REMARK 3 ANGLE : 0.821 1355 REMARK 3 CHIRALITY : 0.056 147 REMARK 3 PLANARITY : 0.007 175 REMARK 3 DIHEDRAL : 12.714 400 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 9WEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300062182. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20530 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 25.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 : 2.870 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 (%): 41.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1M BIS-TRIS PH 5.5, 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291K 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 49.81200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.21450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.21450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.90600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.21450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.21450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.71800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.21450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.21450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.90600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.21450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.21450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.71800 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 49.81200 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: 420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 HOH A 307 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 392 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 GLU A 11 REMARK 465 GLU A 12 REMARK 465 GLY A 13 REMARK 465 MET A 14 REMARK 465 GLU A 133 REMARK 465 GLU A 134 REMARK 465 ALA A 135 REMARK 465 LYS A 136 REMARK 465 ILE A 137 REMARK 465 SER A 138 REMARK 465 LYS A 139 REMARK 465 LEU A 140 REMARK 465 VAL A 141 REMARK 465 LEU A 142 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 91 -159.79 -153.75 REMARK 500 TYR A 96 -119.18 49.75 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 FES A 201 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 FES A 201 S1 115.6 REMARK 620 3 FES A 201 S2 121.9 103.4 REMARK 620 4 CYS A 66 SG 94.8 109.0 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 201 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 78 SG REMARK 620 2 FES A 201 S1 109.5 REMARK 620 3 FES A 201 S2 114.5 103.7 REMARK 620 4 H2S A 203 S 102.8 111.4 115.0 REMARK 620 N 1 2 3 DBREF1 9WEX A 11 142 UNP A0A8B5Y839_BACLI DBREF2 9WEX A A0A8B5Y839 11 142 SEQRES 1 A 132 GLU GLU GLY MET SER ASN GLU SER GLY TYR LEU ARG GLN SEQRES 2 A 132 ILE PHE ASP HIS LEU GLN ASP GLY ILE ILE MET MET ASP SEQRES 3 A 132 GLN GLU ARG THR ILE LEU VAL ILE ASN PRO SER ALA GLU SEQRES 4 A 132 LYS MET THR GLY TRP LYS LEU GLY ASP LYS VAL PRO TYR SEQRES 5 A 132 CYS SER TYR CYS GLN THR ARG LYS LEU GLU ALA GLY GLU SEQRES 6 A 132 GLU ARG CYS TYR LEU LEU ALA LYS ARG GLU ILE PRO TYR SEQRES 7 A 132 PHE LEU SER SER MET PRO THR TYR GLU GLY ARG PHE VAL SEQRES 8 A 132 ASP MET GLU MET SER THR ALA VAL ILE SER GLU ASN GLY SEQRES 9 A 132 ASP GLN MET GLU VAL LEU LEU VAL LEU LYS ASP LEU THR SEQRES 10 A 132 MET LYS LYS LYS GLU GLU GLU ALA LYS ILE SER LYS LEU SEQRES 11 A 132 VAL LEU HET FES A 201 4 HET EDO A 202 4 HET H2S A 203 1 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM EDO 1,2-ETHANEDIOL HETNAM H2S HYDROSULFURIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN H2S HYDROGEN SULFIDE FORMUL 2 FES FE2 S2 FORMUL 3 EDO C2 H6 O2 FORMUL 4 H2S H2 S FORMUL 5 HOH *107(H2 O) HELIX 1 AA1 SER A 15 LEU A 28 1 14 HELIX 2 AA2 ASN A 45 GLY A 53 1 9 HELIX 3 AA3 CYS A 63 ARG A 69 1 7 HELIX 4 AA4 CYS A 78 LYS A 83 1 6 HELIX 5 AA5 LEU A 126 GLU A 132 1 7 SHEET 1 AA1 5 ILE A 41 ILE A 44 0 SHEET 2 AA1 5 GLY A 31 ASP A 36 -1 N MET A 34 O LEU A 42 SHEET 3 AA1 5 GLN A 116 ASP A 125 -1 O LEU A 121 N ILE A 33 SHEET 4 AA1 5 ARG A 99 ASN A 113 -1 N ALA A 108 O LEU A 120 SHEET 5 AA1 5 PHE A 89 THR A 95 -1 N SER A 91 O MET A 103 LINK SG CYS A 63 FE2 FES A 201 1555 1555 2.34 LINK SG CYS A 66 FE2 FES A 201 1555 1555 2.31 LINK SG CYS A 78 FE1 FES A 201 1555 1555 2.32 LINK FE1 FES A 201 S H2S A 203 1555 1555 2.27 CRYST1 50.429 50.429 99.624 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 0.019830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010038 0.00000 CONECT 409 984 CONECT 439 984 CONECT 536 983 CONECT 983 536 985 986 991 CONECT 984 409 439 985 986 CONECT 985 983 984 CONECT 986 983 984 CONECT 987 988 989 CONECT 988 987 CONECT 989 987 990 CONECT 990 989 CONECT 991 983 MASTER 286 0 3 5 5 0 0 6 1067 1 12 11 END