HEADER SIGNALING PROTEIN 25-JUN-23 8JU7 TITLE STRUCTURE OF PSEUDOMONAS AERUGINOSA PARS SENSOR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTIDINE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SENSOR DOMAIN; COMPND 5 EC: 2.7.13.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 SOURCE 5 / 1C / PRS 101 / PAO1; SOURCE 6 GENE: PARS, PA1798; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PSEUDOMONAS AERUGINOSA, TWO-COMPONENT SYSTEM, HISTIDINE KINASE, KEYWDS 2 SENSOR DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.ZHAO,Z.ZHU,Y.SONG,R.BAO REVDAT 2 07-AUG-24 8JU7 1 JRNL REVDAT 1 24-JAN-24 8JU7 0 JRNL AUTH N.L.ZHAO,Z.Q.ZHU,H.Z.FENG,Y.J.SONG,Q.HUANG,X.Y.MOU,C.NONG, JRNL AUTH 2 Y.X.HE,R.BAO JRNL TITL HOST-DERIVED PEPTIDE SIGNALS REGULATE PSEUDOMONAS AERUGINOSA JRNL TITL 2 VIRULENCE STRESS VIA THE PARRS AND CPRRS TWO-COMPONENT JRNL TITL 3 SYSTEMS. JRNL REF J HAZARD MATER V. 460 32512 2023 JRNL REFN ESSN 1873-3336 JRNL PMID 37703740 JRNL DOI 10.1016/J.JHAZMAT.2023.132512 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 17821 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1780 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 25.2700 - 4.2200 0.98 1316 146 0.1917 0.2106 REMARK 3 2 4.2200 - 3.3500 0.96 1240 138 0.1739 0.2359 REMARK 3 3 3.3500 - 2.9300 0.99 1288 143 0.1977 0.2351 REMARK 3 4 2.9300 - 2.6600 0.94 1193 133 0.2059 0.2401 REMARK 3 5 2.6600 - 2.4700 0.98 1248 138 0.2097 0.2887 REMARK 3 6 2.4700 - 2.3300 0.98 1261 140 0.2120 0.2419 REMARK 3 7 2.3300 - 2.2100 0.98 1234 137 0.2026 0.2306 REMARK 3 8 2.2100 - 2.1100 0.95 1204 133 0.1966 0.2822 REMARK 3 9 2.1100 - 2.0300 0.97 1221 136 0.2052 0.2584 REMARK 3 10 2.0300 - 1.9600 0.98 1249 139 0.2075 0.2429 REMARK 3 11 1.9600 - 1.9000 0.97 1228 136 0.2043 0.2512 REMARK 3 12 1.9000 - 1.8500 0.98 1218 136 0.2423 0.2814 REMARK 3 13 1.8500 - 1.8000 0.89 1141 125 0.3009 0.3554 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.86 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 : 0.008 1692 REMARK 3 ANGLE : 0.935 2293 REMARK 3 CHIRALITY : 0.053 251 REMARK 3 PLANARITY : 0.009 306 REMARK 3 DIHEDRAL : 5.560 226 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 8JU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17841 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 17.7100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.70400 REMARK 200 R SYM FOR SHELL (I) : 0.70400 REMARK 200 FOR SHELL : 1.670 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: ALPHAFOLD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1 M BIS-TRIS PH 6.5, 10% W/V POLYETHYLENE GLYCOL REMARK 280 10,000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 15.79700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 THR A 103 REMARK 465 MET B -1 REMARK 465 MET B 0 REMARK 465 SER B 101 REMARK 465 LEU B 102 REMARK 465 THR B 103 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 24 O HOH A 201 1.70 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 ASP A 86 -158.32 -160.63 REMARK 500 ASP B 86 -157.14 -161.39 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JU7 A 1 103 UNP Q9I2U4 Q9I2U4_PSEAE 29 131 DBREF 8JU7 B 1 103 UNP Q9I2U4 Q9I2U4_PSEAE 29 131 SEQADV 8JU7 MET A -1 UNP Q9I2U4 INITIATING METHIONINE SEQADV 8JU7 MET A 0 UNP Q9I2U4 EXPRESSION TAG SEQADV 8JU7 MET B -1 UNP Q9I2U4 INITIATING METHIONINE SEQADV 8JU7 MET B 0 UNP Q9I2U4 EXPRESSION TAG SEQRES 1 A 105 MET MET ALA PHE TYR ASP SER ILE VAL GLU ASN TYR HIS SEQRES 2 A 105 ARG ASP ALA VAL ARG GLY GLN ALA TYR SER LEU VAL GLU SEQRES 3 A 105 LYS LEU ALA PRO LEU ASP GLN ALA GLY ARG GLN ARG GLN SEQRES 4 A 105 LEU GLU ASP TRP ARG PRO HIS TYR GLY LEU GLU LEU SER SEQRES 5 A 105 LEU THR ASP ALA ARG GLN ALA LYS LEU THR GLN GLU GLU SEQRES 6 A 105 GLN ALA LEU LEU ASP LYS ASN LEU LEU VAL VAL ARG GLU SEQRES 7 A 105 ASP PHE THR GLU PHE ILE SER ARG ILE ASP ALA GLY PRO SEQRES 8 A 105 GLN LEU LEU ASP ILE LYS LEU PRO PRO GLU PRO SER LEU SEQRES 9 A 105 THR SEQRES 1 B 105 MET MET ALA PHE TYR ASP SER ILE VAL GLU ASN TYR HIS SEQRES 2 B 105 ARG ASP ALA VAL ARG GLY GLN ALA TYR SER LEU VAL GLU SEQRES 3 B 105 LYS LEU ALA PRO LEU ASP GLN ALA GLY ARG GLN ARG GLN SEQRES 4 B 105 LEU GLU ASP TRP ARG PRO HIS TYR GLY LEU GLU LEU SER SEQRES 5 B 105 LEU THR ASP ALA ARG GLN ALA LYS LEU THR GLN GLU GLU SEQRES 6 B 105 GLN ALA LEU LEU ASP LYS ASN LEU LEU VAL VAL ARG GLU SEQRES 7 B 105 ASP PHE THR GLU PHE ILE SER ARG ILE ASP ALA GLY PRO SEQRES 8 B 105 GLN LEU LEU ASP ILE LYS LEU PRO PRO GLU PRO SER LEU SEQRES 9 B 105 THR FORMUL 3 HOH *94(H2 O) HELIX 1 AA1 PHE A 2 ALA A 27 1 26 HELIX 2 AA2 ASP A 30 ARG A 42 1 13 HELIX 3 AA3 PRO A 43 TYR A 45 5 3 HELIX 4 AA4 ASP A 53 LYS A 58 1 6 HELIX 5 AA5 THR A 60 LYS A 69 1 10 HELIX 6 AA6 PHE B 2 ALA B 27 1 26 HELIX 7 AA7 ASP B 30 ARG B 42 1 13 HELIX 8 AA8 PRO B 43 TYR B 45 5 3 HELIX 9 AA9 ASP B 53 LYS B 58 1 6 HELIX 10 AB1 THR B 60 LYS B 69 1 10 SHEET 1 AA1 4 GLU A 48 THR A 52 0 SHEET 2 AA1 4 LEU A 91 LYS A 95 -1 O ASP A 93 N SER A 50 SHEET 3 AA1 4 GLU A 80 ARG A 84 -1 N PHE A 81 O ILE A 94 SHEET 4 AA1 4 VAL A 73 ARG A 75 -1 N ARG A 75 O GLU A 80 SHEET 1 AA2 4 GLU B 48 THR B 52 0 SHEET 2 AA2 4 LEU B 91 LYS B 95 -1 O ASP B 93 N SER B 50 SHEET 3 AA2 4 GLU B 80 ARG B 84 -1 N PHE B 81 O ILE B 94 SHEET 4 AA2 4 VAL B 73 ARG B 75 -1 N ARG B 75 O GLU B 80 CRYST1 44.444 31.594 71.054 90.00 100.03 90.00 P 1 21 1 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 0.022500 0.000000 0.003978 0.00000 SCALE2 0.000000 0.031652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014292 0.00000