HEADER GENE REGULATION 14-JUL-23 8K3B TITLE THE PSEUDOMONAS AERUGINOSA RCCR PROTEIN COMPLEXED WITH KDPG COMPND MOL_ID: 1; COMPND 2 MOLECULE: MURR/RPIR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATORY PROTEIN RCCR; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: YBBH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.WANG,Z.W.WU,Q.J.JI REVDAT 1 20-DEC-23 8K3B 0 JRNL AUTH Y.J.WANG,Z.W.WU,Q.J.JI JRNL TITL A KDPG SENSOR RCCR GOVERNS PSEUDOMONAS AERUGINOSA CARBON JRNL TITL 2 METABOLISM AND AMINOGLYCOSIDE ANTIBIOTIC TOLERANCE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 75.2 REMARK 3 NUMBER OF REFLECTIONS : 25023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1357 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 1.9500 - 1.9010 0.35 851 44 0.2690 0.2910 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8K3B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039450. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-20 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26374 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.2 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.65200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 64.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M DL-MALIC ACID PH 7.0, 0.1 M REMARK 280 IMIDAZOLE PH 7.0, 22% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550 REMARK 280 (V/V), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.81200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.94400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.81200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.94400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.81200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.94400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.06900 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.81200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.94400 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: 6770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 -1.000000 0.000000 0.000000 78.13800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 81.62400 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 HOH A 452 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 498 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 552 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 556 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 VAL A 282 REMARK 465 MET A 283 REMARK 465 LYS A 284 REMARK 465 ASN A 285 REMARK 465 GLN A 286 REMARK 465 GLU A 287 REMARK 465 GLU A 288 REMARK 465 ARG A 289 REMARK 465 GLY A 290 REMARK 465 GLU A 291 REMARK 465 PRO A 292 REMARK 465 SER A 293 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 GLU A 87 -30.57 -37.23 REMARK 500 LEU A 153 33.83 -99.93 REMARK 500 ASP A 226 56.79 -106.43 REMARK 500 LEU A 237 -72.24 -144.39 REMARK 500 LEU A 278 151.33 -49.60 REMARK 500 REMARK 500 REMARK: NULL 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 556 DISTANCE = 6.48 ANGSTROMS DBREF1 8K3B A 1 293 UNP A0A071KWR3_PSEAI DBREF2 8K3B A A0A071KWR3 1 293 SEQRES 1 A 293 MET ASN LEU LEU GLN HIS ILE ALA GLN SER ARG GLN GLN SEQRES 2 A 293 LEU ARG LYS SER GLU LEU LYS VAL ALA ASP HIS VAL LEU SEQRES 3 A 293 ASN ASP PRO ALA SER VAL MET HIS SER SER MET ALA GLU SEQRES 4 A 293 LEU ALA HIS GLY VAL GLY VAL SER GLU PRO THR ILE VAL SEQRES 5 A 293 ARG PHE CYS ARG ALA ILE GLY CYS SER GLY PHE GLN ASP SEQRES 6 A 293 LEU LYS LEU LYS LEU ALA GLN SER LEU ALA ALA GLY ALA SEQRES 7 A 293 SER PHE GLY GLN PHE SER ILE HIS GLU SER ASP SER VAL SEQRES 8 A 293 ALA ASP PHE SER LEU LYS ILE PHE ASP THR THR LEU HIS SEQRES 9 A 293 SER LEU MET GLU VAL ARG GLU HIS LEU ASP THR HIS ALA SEQRES 10 A 293 LEU GLU ARG ALA ILE ALA ALA ILE ALA HIS ALA GLN ARG SEQRES 11 A 293 VAL GLU PHE TYR GLY PHE GLY ALA SER GLY ALA VAL ALA SEQRES 12 A 293 SER ASP ALA GLN HIS LYS PHE PHE ARG LEU LEU LEU SER SEQRES 13 A 293 ALA ALA ALA TYR SER ASP PRO HIS MET GLN ALA MET SER SEQRES 14 A 293 ALA VAL THR LEU LYS PRO SER ASP VAL ALA ILE CYS ILE SEQRES 15 A 293 SER GLN SER GLY ARG SER LYS ASP LEU LEU ILE THR ALA SEQRES 16 A 293 ASN LEU VAL ARG GLU ALA GLY ALA THR LEU ILE THR LEU SEQRES 17 A 293 CYS PRO SER GLN THR PRO LEU ALA ASP LEU ALA THR VAL SEQRES 18 A 293 ASN LEU ALA ILE ASP VAL HIS GLU ASP THR ASP ILE TYR SEQRES 19 A 293 THR PRO LEU THR SER ARG ILE ALA HIS LEU VAL VAL ILE SEQRES 20 A 293 ASP VAL LEU ALA MET GLY VAL ALA MET ALA ARG GLY PRO SEQRES 21 A 293 ASP LEU VAL ASN HIS LEU LYS SER VAL LYS ARG SER LEU SEQRES 22 A 293 ARG SER LEU ARG LEU SER PRO LYS VAL MET LYS ASN GLN SEQRES 23 A 293 GLU GLU ARG GLY GLU PRO SER HET ELE A 301 16 HETNAM ELE 2-KETO 3 DEOXY 6 PHOSPHO GLUCONATE FORMUL 2 ELE C6 H11 O9 P FORMUL 3 HOH *156(H2 O) HELIX 1 AA1 ASN A 2 ARG A 11 1 10 HELIX 2 AA2 GLN A 12 LEU A 14 5 3 HELIX 3 AA3 ARG A 15 ASP A 28 1 14 HELIX 4 AA4 ASP A 28 MET A 33 1 6 HELIX 5 AA5 SER A 36 GLY A 45 1 10 HELIX 6 AA6 SER A 47 ILE A 58 1 12 HELIX 7 AA7 GLY A 62 GLN A 72 1 11 HELIX 8 AA8 ALA A 75 GLY A 81 1 7 HELIX 9 AA9 SER A 90 HIS A 112 1 23 HELIX 10 AB1 ASP A 114 ALA A 128 1 15 HELIX 11 AB2 GLY A 137 PHE A 151 1 15 HELIX 12 AB3 ASP A 162 VAL A 171 1 10 HELIX 13 AB4 SER A 188 ALA A 201 1 14 HELIX 14 AB5 THR A 213 ALA A 219 1 7 HELIX 15 AB6 LEU A 237 ALA A 257 1 21 HELIX 16 AB7 ASP A 261 SER A 272 1 12 HELIX 17 AB8 LEU A 273 ARG A 277 5 5 SHEET 1 AA1 5 SER A 156 TYR A 160 0 SHEET 2 AA1 5 ARG A 130 TYR A 134 1 N VAL A 131 O SER A 156 SHEET 3 AA1 5 VAL A 178 ILE A 182 1 O ILE A 180 N TYR A 134 SHEET 4 AA1 5 THR A 204 LEU A 208 1 O ILE A 206 N ALA A 179 SHEET 5 AA1 5 VAL A 221 ASN A 222 1 O VAL A 221 N THR A 207 CRYST1 78.138 81.624 137.888 90.00 90.00 90.00 I 2 2 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 0.012798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007252 0.00000