HEADER HYDROLASE ACTIVATOR 01-APR-03 1OX8 TITLE CRYSTAL STRUCTURE OF SSPB COMPND MOL_ID: 1; COMPND 2 MOLECULE: STRINGENT STARVATION PROTEIN B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 5-111; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 STRAIN: O157:H7; SOURCE 5 GENE: SSPB OR B3228 OR Z4586 OR ECS4101; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA-BINDING PROPERTY, HYDROLASE ACTIVATOR EXPDTA X-RAY DIFFRACTION AUTHOR H.K.SONG,M.J.ECK REVDAT 3 13-JUL-11 1OX8 1 VERSN REVDAT 2 24-FEB-09 1OX8 1 VERSN REVDAT 1 26-AUG-03 1OX8 0 JRNL AUTH H.K.SONG,M.J.ECK JRNL TITL STRUCTURAL BASIS OF DEGRADATION SIGNAL RECOGNITION BY SSPB, JRNL TITL 2 A SPECIFICITY-ENHANCING FACTOR FOR THE CLPXP PROTEOLYTIC JRNL TITL 3 MACHINE JRNL REF MOL.CELL V. 12 75 2003 JRNL REFN ISSN 1097-2765 JRNL PMID 12887894 JRNL DOI 10.1016/S1097-2765(03)00271-5 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 9.0 REMARK 3 NUMBER OF REFLECTIONS : 15100 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1649 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1686 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 144 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.38 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OX8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-03. REMARK 100 THE RCSB ID CODE IS RCSB018765. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-02 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 : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18454 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 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 : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 93.99200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.05800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.05800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 140.98800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.05800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.05800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.99600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.05800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.05800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 140.98800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.05800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.05800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.99600 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 93.99200 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: 1450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 ALA A 59 2.59 -57.20 REMARK 500 ASN A 98 14.90 -147.23 REMARK 500 ALA A 109 -15.96 -42.97 REMARK 500 GLU B 97 -74.23 -67.30 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 B 176 DISTANCE = 5.46 ANGSTROMS REMARK 525 HOH B 179 DISTANCE = 5.54 ANGSTROMS DBREF 1OX8 A 5 111 UNP P25663 SSPB_ECOLI 5 111 DBREF 1OX8 B 5 111 UNP P25663 SSPB_ECOLI 5 111 SEQADV 1OX8 MSE A 43 UNP P25663 MET 43 MODIFIED RESIDUE SEQADV 1OX8 MSE A 103 UNP P25663 MET 103 MODIFIED RESIDUE SEQADV 1OX8 MSE B 43 UNP P25663 MET 43 MODIFIED RESIDUE SEQADV 1OX8 MSE B 103 UNP P25663 MET 103 MODIFIED RESIDUE SEQRES 1 A 107 GLN LEU THR PRO ARG ARG PRO TYR LEU LEU ARG ALA PHE SEQRES 2 A 107 TYR GLU TRP LEU LEU ASP ASN GLN LEU THR PRO HIS LEU SEQRES 3 A 107 VAL VAL ASP VAL THR LEU PRO GLY VAL GLN VAL PRO MSE SEQRES 4 A 107 GLU TYR ALA ARG ASP GLY GLN ILE VAL LEU ASN ILE ALA SEQRES 5 A 107 PRO ARG ALA VAL GLY ASN LEU GLU LEU ALA ASN ASP GLU SEQRES 6 A 107 VAL ARG PHE ASN ALA ARG PHE GLY GLY ILE PRO ARG GLN SEQRES 7 A 107 VAL SER VAL PRO LEU ALA ALA VAL LEU ALA ILE TYR ALA SEQRES 8 A 107 ARG GLU ASN GLY ALA GLY THR MSE PHE GLU PRO GLU ALA SEQRES 9 A 107 ALA TYR ASP SEQRES 1 B 107 GLN LEU THR PRO ARG ARG PRO TYR LEU LEU ARG ALA PHE SEQRES 2 B 107 TYR GLU TRP LEU LEU ASP ASN GLN LEU THR PRO HIS LEU SEQRES 3 B 107 VAL VAL ASP VAL THR LEU PRO GLY VAL GLN VAL PRO MSE SEQRES 4 B 107 GLU TYR ALA ARG ASP GLY GLN ILE VAL LEU ASN ILE ALA SEQRES 5 B 107 PRO ARG ALA VAL GLY ASN LEU GLU LEU ALA ASN ASP GLU SEQRES 6 B 107 VAL ARG PHE ASN ALA ARG PHE GLY GLY ILE PRO ARG GLN SEQRES 7 B 107 VAL SER VAL PRO LEU ALA ALA VAL LEU ALA ILE TYR ALA SEQRES 8 B 107 ARG GLU ASN GLY ALA GLY THR MSE PHE GLU PRO GLU ALA SEQRES 9 B 107 ALA TYR ASP MODRES 1OX8 MSE A 43 MET SELENOMETHIONINE MODRES 1OX8 MSE A 103 MET SELENOMETHIONINE MODRES 1OX8 MSE B 43 MET SELENOMETHIONINE MODRES 1OX8 MSE B 103 MET SELENOMETHIONINE HET MSE A 43 8 HET MSE A 103 8 HET MSE B 43 8 HET MSE B 103 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *144(H2 O) HELIX 1 1 ARG A 9 ASN A 24 1 16 HELIX 2 2 PRO A 42 ALA A 46 5 5 HELIX 3 3 GLU A 107 ASP A 111 5 5 HELIX 4 4 ARG B 9 ASN B 24 1 16 HELIX 5 5 PRO B 42 ALA B 46 5 5 HELIX 6 6 GLU B 107 ASP B 111 5 5 SHEET 1 A 4 GLN A 50 ASN A 54 0 SHEET 2 A 4 PRO A 28 ASP A 33 -1 N LEU A 30 O LEU A 53 SHEET 3 A 4 VAL A 90 ALA A 95 -1 O LEU A 91 N VAL A 31 SHEET 4 A 4 GLY A 101 MSE A 103 -1 O THR A 102 N ILE A 93 SHEET 1 B 3 GLY A 61 LEU A 65 0 SHEET 2 B 3 GLU A 69 ARG A 75 -1 O ARG A 71 N GLU A 64 SHEET 3 B 3 PRO A 80 PRO A 86 -1 O ARG A 81 N ALA A 74 SHEET 1 C 4 GLN B 50 ASN B 54 0 SHEET 2 C 4 PRO B 28 ASP B 33 -1 N LEU B 30 O LEU B 53 SHEET 3 C 4 VAL B 90 ALA B 95 -1 O ALA B 92 N VAL B 31 SHEET 4 C 4 GLY B 101 MSE B 103 -1 O THR B 102 N ILE B 93 SHEET 1 D 3 GLY B 61 LEU B 65 0 SHEET 2 D 3 GLU B 69 PHE B 76 -1 O ARG B 71 N GLU B 64 SHEET 3 D 3 ILE B 79 PRO B 86 -1 O VAL B 83 N PHE B 72 LINK C PRO A 42 N MSE A 43 1555 1555 1.33 LINK C MSE A 43 N GLU A 44 1555 1555 1.33 LINK C THR A 102 N MSE A 103 1555 1555 1.33 LINK C MSE A 103 N PHE A 104 1555 1555 1.32 LINK C PRO B 42 N MSE B 43 1555 1555 1.33 LINK C MSE B 43 N GLU B 44 1555 1555 1.33 LINK C THR B 102 N MSE B 103 1555 1555 1.33 LINK C MSE B 103 N PHE B 104 1555 1555 1.32 CRYST1 60.116 60.116 187.984 90.00 90.00 90.00 P 43 21 2 16 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 0.016635 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016635 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005320 0.00000