HEADER SIGNALING PROTEIN 26-SEP-08 3EOD TITLE CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF E. COLI RSSB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN HNR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESPONSE REGULATORY DOMAIN, UNP RESIDUES 1-130; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: B1235, HNR, JW1223, RSSB, YCHL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RESPONSE REGULATOR, PHOSPHOPROTEIN, TWO-COMPONENT REGULATORY SYSTEM, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.LEVCHENKO,R.A.GRANT,R.T.SAUER,T.A.BAKER REVDAT 4 21-FEB-24 3EOD 1 REMARK REVDAT 3 24-JAN-18 3EOD 1 JRNL REVDAT 2 25-OCT-17 3EOD 1 REMARK REVDAT 1 06-OCT-09 3EOD 0 JRNL AUTH I.LEVCHENKO,R.A.GRANT,R.T.SAUER,T.A.BAKER JRNL TITL THE STRUCTURE OF RSSB, A CLPX ADAPTOR PROTEIN THAT REGULATES JRNL TITL 2 SIGMA S JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.180 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1221 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 39.0800 - 3.6380 0.95 1227 164 0.2280 0.2600 REMARK 3 2 3.6380 - 2.8880 1.00 1224 142 0.2130 0.2440 REMARK 3 3 2.8880 - 2.5230 1.00 1192 143 0.2340 0.2590 REMARK 3 4 2.5230 - 2.2920 1.00 1226 109 0.2160 0.2640 REMARK 3 5 2.2920 - 2.1280 1.00 1190 134 0.2040 0.2600 REMARK 3 6 2.1280 - 2.0030 0.99 1180 134 0.2110 0.2250 REMARK 3 7 2.0030 - 1.9020 0.99 1149 136 0.2170 0.2870 REMARK 3 8 1.9020 - 1.8200 0.97 1150 138 0.2310 0.2710 REMARK 3 9 1.8200 - 1.7500 0.94 1095 121 0.2460 0.2880 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 80.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 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) : 58.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.38600 REMARK 3 B22 (A**2) : -5.38600 REMARK 3 B33 (A**2) : -15.91300 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 : 0.004 961 REMARK 3 ANGLE : 0.839 1315 REMARK 3 CHIRALITY : 0.050 162 REMARK 3 PLANARITY : 0.004 169 REMARK 3 DIHEDRAL : 13.330 380 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 3EOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000049572. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.75 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) : 0.97932,1.0070,1.0087 REMARK 200 MONOCHROMATOR : CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12003 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 38.60 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 80.7330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 23.50 REMARK 200 R MERGE FOR SHELL (I) : 0.46400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, 0.2 NA ACETATE, 1 MM REMARK 280 DTT, 28% PEG3350, 1.9 MG/ML PROTEIN, PH 8.75, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 64.53133 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 32.26567 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 32.26567 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 64.53133 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 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 178 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 MET A 1 REMARK 465 THR A 2 REMARK 465 MET A 61 REMARK 465 PRO A 62 REMARK 465 ARG A 63 REMARK 465 MET A 64 REMARK 465 ASN A 65 REMARK 465 LYS A 111 REMARK 465 ASP A 112 REMARK 465 LEU A 113 REMARK 465 PRO A 126 REMARK 465 SER A 127 REMARK 465 MET A 128 REMARK 465 PHE A 129 REMARK 465 ASN A 130 DBREF 3EOD A 1 130 UNP P0AEV1 HNR_ECOLI 1 130 SEQRES 1 A 130 MET THR GLN PRO LEU VAL GLY LYS GLN ILE LEU ILE VAL SEQRES 2 A 130 GLU ASP GLU GLN VAL PHE ARG SER LEU LEU ASP SER TRP SEQRES 3 A 130 PHE SER SER LEU GLY ALA THR THR VAL LEU ALA ALA ASP SEQRES 4 A 130 GLY VAL ASP ALA LEU GLU LEU LEU GLY GLY PHE THR PRO SEQRES 5 A 130 ASP LEU MET ILE CYS ASP ILE ALA MET PRO ARG MET ASN SEQRES 6 A 130 GLY LEU LYS LEU LEU GLU HIS ILE ARG ASN ARG GLY ASP SEQRES 7 A 130 GLN THR PRO VAL LEU VAL ILE SER ALA THR GLU ASN MET SEQRES 8 A 130 ALA ASP ILE ALA LYS ALA LEU ARG LEU GLY VAL GLU ASP SEQRES 9 A 130 VAL LEU LEU LYS PRO VAL LYS ASP LEU ASN ARG LEU ARG SEQRES 10 A 130 GLU MET VAL PHE ALA CYS LEU TYR PRO SER MET PHE ASN FORMUL 2 HOH *52(H2 O) HELIX 1 1 GLU A 16 LEU A 30 1 15 HELIX 2 2 ASP A 39 GLY A 48 1 10 HELIX 3 3 GLY A 66 ARG A 76 1 11 HELIX 4 4 ASN A 90 GLY A 101 1 12 HELIX 5 5 ASN A 114 TYR A 125 1 12 SHEET 1 A 5 THR A 33 ALA A 37 0 SHEET 2 A 5 GLN A 9 VAL A 13 1 N ILE A 12 O VAL A 35 SHEET 3 A 5 LEU A 54 CYS A 57 1 O ILE A 56 N VAL A 13 SHEET 4 A 5 VAL A 82 SER A 86 1 O LEU A 83 N MET A 55 SHEET 5 A 5 ASP A 104 LEU A 107 1 O LEU A 106 N VAL A 84 CISPEP 1 LYS A 108 PRO A 109 0 0.48 CISPEP 2 LYS A 108 PRO A 109 0 0.45 CRYST1 45.114 45.114 96.797 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 0.022166 0.012798 0.000000 0.00000 SCALE2 0.000000 0.025595 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010331 0.00000