HEADER PEPTIDE BINDING PROTEIN 23-MAR-09 3GQ0 TITLE THE STRUCTURE OF THE CAULOBACTER CRESCENTUS CLPS PROTEASE ADAPTOR TITLE 2 PROTEIN - APO STRUCTURE WITH NO PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES; SOURCE 3 ORGANISM_COMMON: CAULOBACTER VIBRIOIDES; SOURCE 4 ORGANISM_TAXID: 155892; SOURCE 5 STRAIN: CB15; SOURCE 6 GENE: CC_2467, CLPS; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET23B KEYWDS ADAPTOR, PROTEIN-PEPTIDE COMPLEX, PEPTIDE-BINDING PROTEIN, PEPTIDE KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.A.BAKER,G.ROMAN-HERNANDEZ,R.T.SAUER,R.A.GRANT REVDAT 4 06-SEP-23 3GQ0 1 REMARK REVDAT 3 01-NOV-17 3GQ0 1 REMARK REVDAT 2 30-JUN-09 3GQ0 1 JRNL REVDAT 1 28-APR-09 3GQ0 0 JRNL AUTH G.ROMAN-HERNANDEZ,R.A.GRANT,R.T.SAUER,T.A.BAKER JRNL TITL MOLECULAR BASIS OF SUBSTRATE SELECTION BY THE N-END RULE JRNL TITL 2 ADAPTOR PROTEIN CLPS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 106 8888 2009 JRNL REFN ISSN 0027-8424 JRNL PMID 19451643 JRNL DOI 10.1073/PNAS.0903614106 REMARK 2 REMARK 2 RESOLUTION. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 7799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 366 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 32.7760 - 2.9790 0.99 2633 120 0.2060 0.2460 REMARK 3 2 2.9790 - 2.3650 0.96 2512 123 0.2320 0.2840 REMARK 3 3 2.3650 - 2.0660 0.89 2288 123 0.2540 0.2980 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 : 0.34 REMARK 3 B_SOL : 45.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.360 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) : 37.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.95300 REMARK 3 B22 (A**2) : -9.03400 REMARK 3 B33 (A**2) : 5.08200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 13.82100 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 1382 REMARK 3 ANGLE : 0.712 1873 REMARK 3 CHIRALITY : 0.046 210 REMARK 3 PLANARITY : 0.003 243 REMARK 3 DIHEDRAL : 14.506 504 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: chain A and (resseq 39:95 or resseq REMARK 3 97:119 ) REMARK 3 SELECTION : chain B and (resseq 39:95 or resseq REMARK 3 97:119 ) REMARK 3 ATOM PAIRS NUMBER : 658 REMARK 3 RMSD : 0.012 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GQ0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052169. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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-E 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 : CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : VARIMAX-HR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.50 REMARK 200 R MERGE (I) : 0.14100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8160 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.43500 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3DNJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 0.025 M MGCL2, REMARK 280 14% PEG 3350, VAPOR DIFFUSION, TEMPERATURE 300K 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 19.23950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 35 REMARK 465 GLN A 36 REMARK 465 LYS A 37 REMARK 465 THR B 35 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN B 36 CG CD OE1 NE2 REMARK 470 LYS B 37 CG CD CE NZ 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 TYR A 50 -38.70 -131.77 REMARK 500 SER B 39 139.45 -35.12 REMARK 500 TYR B 50 -38.70 -131.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DNJ RELATED DB: PDB REMARK 900 SAME PROTEIN WITH Y PEPTIDE REMARK 900 RELATED ID: 3G19 RELATED DB: PDB REMARK 900 SAME PROTEIN WITH L PEPTIDE REMARK 900 RELATED ID: 3G1B RELATED DB: PDB REMARK 900 M53A MUTANT WITH W PEPTIDE REMARK 900 RELATED ID: 3GQ1 RELATED DB: PDB DBREF 3GQ0 A 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 DBREF 3GQ0 B 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 SEQRES 1 A 85 THR GLN LYS PRO SER LEU TYR ARG VAL LEU ILE LEU ASN SEQRES 2 A 85 ASP ASP TYR THR PRO MET GLU PHE VAL VAL TYR VAL LEU SEQRES 3 A 85 GLU ARG PHE PHE ASN LYS SER ARG GLU ASP ALA THR ARG SEQRES 4 A 85 ILE MET LEU HIS VAL HIS GLN ASN GLY VAL GLY VAL CYS SEQRES 5 A 85 GLY VAL TYR THR TYR GLU VAL ALA GLU THR LYS VAL ALA SEQRES 6 A 85 GLN VAL ILE ASP SER ALA ARG ARG HIS GLN HIS PRO LEU SEQRES 7 A 85 GLN CYS THR MET GLU LYS ASP SEQRES 1 B 85 THR GLN LYS PRO SER LEU TYR ARG VAL LEU ILE LEU ASN SEQRES 2 B 85 ASP ASP TYR THR PRO MET GLU PHE VAL VAL TYR VAL LEU SEQRES 3 B 85 GLU ARG PHE PHE ASN LYS SER ARG GLU ASP ALA THR ARG SEQRES 4 B 85 ILE MET LEU HIS VAL HIS GLN ASN GLY VAL GLY VAL CYS SEQRES 5 B 85 GLY VAL TYR THR TYR GLU VAL ALA GLU THR LYS VAL ALA SEQRES 6 B 85 GLN VAL ILE ASP SER ALA ARG ARG HIS GLN HIS PRO LEU SEQRES 7 B 85 GLN CYS THR MET GLU LYS ASP FORMUL 3 HOH *46(H2 O) HELIX 1 1 PRO A 52 ASN A 65 1 14 HELIX 2 2 SER A 67 GLY A 82 1 16 HELIX 3 3 THR A 90 HIS A 108 1 19 HELIX 4 4 PRO B 52 ASN B 65 1 14 HELIX 5 5 SER B 67 GLY B 82 1 16 HELIX 6 6 THR B 90 HIS B 108 1 19 SHEET 1 A 3 VAL A 83 TYR A 89 0 SHEET 2 A 3 TYR A 41 LEU A 46 -1 N TYR A 41 O TYR A 89 SHEET 3 A 3 GLN A 113 LYS A 118 -1 O THR A 115 N LEU A 44 SHEET 1 B 3 VAL B 83 TYR B 89 0 SHEET 2 B 3 TYR B 41 LEU B 46 -1 N TYR B 41 O TYR B 89 SHEET 3 B 3 GLN B 113 LYS B 118 -1 O THR B 115 N LEU B 44 CRYST1 27.667 38.479 62.560 90.00 88.42 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 0.036144 0.000000 -0.000999 0.00000 SCALE2 0.000000 0.025988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015991 0.00000