HEADER SIGNALING PROTEIN 11-JAN-21 7LCM TITLE RECEIVER DOMAIN OF RSSB BOUND TO BERYLLOFLUORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATOR OF RPOS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: MG1655; SOURCE 5 GENE: RSSB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RECEIVER DOMAIN, RESPONSE REGULATOR, CLPXP ADAPTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.DEACONESCU,J.SCHWARTZ,J.SON REVDAT 2 18-OCT-23 7LCM 1 REMARK REVDAT 1 07-APR-21 7LCM 0 JRNL AUTH J.SCHWARTZ,J.SON,C.BRUGGER,A.M.DEACONESCU JRNL TITL PHOSPHO-DEPENDENT SIGNALING DURING THE GENERAL STRESS JRNL TITL 2 RESPONSE BY THE ATYPICAL RESPONSE REGULATOR AND CLPXP JRNL TITL 3 ADAPTOR RSSB. JRNL REF PROTEIN SCI. V. 30 899 2021 JRNL REFN ESSN 1469-896X JRNL PMID 33599047 JRNL DOI 10.1002/PRO.4047 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4080 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 9732 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 968 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 40.1200 - 3.6500 1.00 1353 148 0.1847 0.2256 REMARK 3 2 3.6500 - 2.9000 1.00 1264 138 0.2057 0.2464 REMARK 3 3 2.9000 - 2.5300 1.00 1258 140 0.2331 0.2571 REMARK 3 4 2.5300 - 2.3000 1.00 1241 137 0.2054 0.2719 REMARK 3 5 2.3000 - 2.1300 1.00 1233 137 0.2045 0.2652 REMARK 3 6 2.1300 - 2.0100 1.00 1208 136 0.2155 0.2666 REMARK 3 7 2.0100 - 1.9100 0.96 1207 132 0.2533 0.3049 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) : 0.159 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.134 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.01 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 1004 REMARK 3 ANGLE : 1.104 1359 REMARK 3 CHIRALITY : 0.064 165 REMARK 3 PLANARITY : 0.009 173 REMARK 3 DIHEDRAL : 5.655 135 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 12.0059 -10.5907 9.2383 REMARK 3 T TENSOR REMARK 3 T11: 0.2995 T22: 0.2517 REMARK 3 T33: 0.2925 T12: -0.0173 REMARK 3 T13: 0.0255 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 1.8528 L22: 2.7179 REMARK 3 L33: 2.1439 L12: -1.0301 REMARK 3 L13: -0.2279 L23: 1.2364 REMARK 3 S TENSOR REMARK 3 S11: -0.1183 S12: 0.2178 S13: -0.2601 REMARK 3 S21: -0.1341 S22: -0.0225 S23: 0.1770 REMARK 3 S31: 0.2212 S32: -0.1200 S33: 0.1245 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 7LCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000254076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C 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 EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9736 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.120 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : 1.700 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: 7L9C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 22% PEG 3,350, REMARK 280 AND 0.1M TRIS-HCL PH 8.8, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.92733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.96367 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 31.96367 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.92733 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: 2270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 31.96367 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 327 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 -2 REMARK 465 PRO A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 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 GLN A 79 O HOH A 301 2.09 REMARK 500 O HOH A 302 O HOH A 307 2.14 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 ILE A 59 -61.85 -100.17 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 15 OD1 REMARK 620 2 ASP A 58 OD2 85.9 REMARK 620 3 ALA A 60 O 92.8 85.6 REMARK 620 4 HOH A 314 O 90.2 92.5 176.3 REMARK 620 5 HOH A 326 O 94.1 175.7 90.2 91.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BEF A 202 BE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 58 OD1 REMARK 620 2 BEF A 202 F1 97.0 REMARK 620 3 BEF A 202 F2 107.4 112.4 REMARK 620 4 BEF A 202 F3 109.1 114.0 115.1 REMARK 620 N 1 2 3 DBREF 7LCM A 1 129 UNP P0AEV1 RSSB_ECOLI 1 129 SEQADV 7LCM GLY A -2 UNP P0AEV1 EXPRESSION TAG SEQADV 7LCM PRO A -1 UNP P0AEV1 EXPRESSION TAG SEQADV 7LCM HIS A 0 UNP P0AEV1 EXPRESSION TAG SEQRES 1 A 132 GLY PRO HIS MET THR GLN PRO LEU VAL GLY LYS GLN ILE SEQRES 2 A 132 LEU ILE VAL GLU ASP GLU GLN VAL PHE ARG SER LEU LEU SEQRES 3 A 132 ASP SER TRP PHE SER SER LEU GLY ALA THR THR VAL LEU SEQRES 4 A 132 ALA ALA ASP GLY VAL ASP ALA LEU GLU LEU LEU GLY GLY SEQRES 5 A 132 PHE THR PRO ASP LEU MET ILE CYS ASP ILE ALA MET PRO SEQRES 6 A 132 ARG MET ASN GLY LEU LYS LEU LEU GLU HIS ILE ARG ASN SEQRES 7 A 132 ARG GLY ASP GLN THR PRO VAL LEU VAL ILE SER ALA THR SEQRES 8 A 132 GLU ASN MET ALA ASP ILE ALA LYS ALA LEU ARG LEU GLY SEQRES 9 A 132 VAL GLU ASP VAL LEU LEU LYS PRO VAL LYS ASP LEU ASN SEQRES 10 A 132 ARG LEU ARG GLU MET VAL PHE ALA CYS LEU TYR PRO SER SEQRES 11 A 132 MET PHE HET MG A 201 1 HET BEF A 202 4 HETNAM MG MAGNESIUM ION HETNAM BEF BERYLLIUM TRIFLUORIDE ION FORMUL 2 MG MG 2+ FORMUL 3 BEF BE F3 1- FORMUL 4 HOH *44(H2 O) HELIX 1 AA1 GLU A 16 LEU A 30 1 15 HELIX 2 AA2 ASP A 39 GLY A 48 1 10 HELIX 3 AA3 ASN A 65 ARG A 76 1 12 HELIX 4 AA4 ASN A 90 LEU A 100 1 11 HELIX 5 AA5 ASP A 112 TYR A 125 1 14 SHEET 1 AA1 5 THR A 33 ALA A 37 0 SHEET 2 AA1 5 GLN A 9 VAL A 13 1 N ILE A 12 O VAL A 35 SHEET 3 AA1 5 LEU A 54 CYS A 57 1 O ILE A 56 N LEU A 11 SHEET 4 AA1 5 VAL A 82 SER A 86 1 O LEU A 83 N MET A 55 SHEET 5 AA1 5 ASP A 104 LEU A 107 1 O LEU A 106 N VAL A 84 LINK OD1 ASP A 15 MG MG A 201 1555 1555 2.08 LINK OD2 ASP A 58 MG MG A 201 1555 1555 2.04 LINK OD1 ASP A 58 BE BEF A 202 1555 1555 1.99 LINK O ALA A 60 MG MG A 201 1555 1555 2.06 LINK MG MG A 201 O HOH A 314 1555 1555 2.06 LINK MG MG A 201 O HOH A 326 1555 1555 1.93 CISPEP 1 LYS A 108 PRO A 109 0 -6.74 CRYST1 46.329 46.329 95.891 90.00 90.00 120.00 P 32 2 1 6 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 0.021585 0.012462 0.000000 0.00000 SCALE2 0.000000 0.024924 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010429 0.00000