HEADER PEPTIDE BINDING PROTEIN 31-MAR-09 3GW1 TITLE THE STRUCTURE OF THE CAULOBACTER CRESCENTUS CLPS PROTEASE ADAPTOR TITLE 2 PROTEIN IN COMPLEX WITH FGG TRIPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: FGG PEPTIDE; COMPND 7 CHAIN: C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES; SOURCE 3 ORGANISM_TAXID: 155892; SOURCE 4 STRAIN: CB15; SOURCE 5 GENE: CLPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET23B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES 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 3GW1 1 COMPND SOURCE DBREF REVDAT 3 01-NOV-17 3GW1 1 REMARK REVDAT 2 30-JUN-09 3GW1 1 JRNL REVDAT 1 05-MAY-09 3GW1 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. 2.36 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) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.2 REMARK 3 NUMBER OF REFLECTIONS : 4884 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.272 REMARK 3 R VALUE (WORKING SET) : 0.270 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.520 REMARK 3 FREE R VALUE TEST SET COUNT : 221 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 32.7223 - 2.9727 0.95 2535 120 0.2453 0.2640 REMARK 3 2 2.9727 - 2.3597 0.81 2128 101 0.3266 0.3725 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 : 0.35 REMARK 3 B_SOL : 48.60 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 1408 REMARK 3 ANGLE : 0.670 1904 REMARK 3 CHIRALITY : 0.047 212 REMARK 3 PLANARITY : 0.003 245 REMARK 3 DIHEDRAL : 19.100 512 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 38:119 ) REMARK 3 SELECTION : CHAIN B AND (RESSEQ 38:119 ) REMARK 3 ATOM PAIRS NUMBER : 667 REMARK 3 RMSD : 0.016 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052377. 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 : CRYSTAL MONOCHROMATOR 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 : 4895 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9330 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.31800 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: NULL REMARK 200 STARTING MODEL: 3DNJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 0.2 M MGCL2, REMARK 280 25% 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 19.16000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 465 GLN B 36 REMARK 465 LYS B 37 REMARK 465 GLY C 3 REMARK 465 GLY D 3 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 117 138.56 -175.78 REMARK 500 GLU B 117 139.47 -174.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DNJ RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH PEPTIDE CONTAINING Y N-TERMINAL RESIDUE REMARK 900 RELATED ID: 3G19 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH PEPTIDE CONTAINING L N-TERMINAL RESIDUE REMARK 900 RELATED ID: 3GQ1 RELATED DB: PDB REMARK 900 SAME PROTEIN IN COMPLEX WITH PEPTIDE CONTAINING W N-TERMINAL RESIDUE REMARK 900 RELATED ID: 3G1B RELATED DB: PDB REMARK 900 M53A MUTANT PROTEIN IN COMPLEX WITH PEPTIDE CONTAINING W N-TERMINAL REMARK 900 RESIDUE REMARK 900 RELATED ID: 3GQ0 RELATED DB: PDB REMARK 900 APO PROTEIN NO PEPTIDE BOUNT DBREF1 3GW1 A 35 119 UNP A0A290MK63_CAUVI DBREF2 3GW1 A A0A290MK63 25 109 DBREF1 3GW1 B 35 119 UNP A0A290MK63_CAUVI DBREF2 3GW1 B A0A290MK63 25 109 DBREF 3GW1 C 1 3 PDB 3GW1 3GW1 1 3 DBREF 3GW1 D 1 3 PDB 3GW1 3GW1 1 3 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 SEQRES 1 C 3 PHE GLY GLY SEQRES 1 D 3 PHE GLY GLY HET MG A 1 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG MG 2+ FORMUL 6 HOH *25(H2 O) HELIX 1 1 PRO A 52 PHE A 64 1 13 HELIX 2 2 SER A 67 GLY A 82 1 16 HELIX 3 3 TYR A 91 HIS A 108 1 18 HELIX 4 4 PRO B 52 PHE B 64 1 13 HELIX 5 5 SER B 67 GLY B 82 1 16 HELIX 6 6 TYR B 91 HIS B 108 1 18 SHEET 1 A 3 VAL A 83 THR A 90 0 SHEET 2 A 3 LEU A 40 LEU A 46 -1 N VAL A 43 O CYS A 86 SHEET 3 A 3 GLN A 113 LYS A 118 -1 O GLU A 117 N ARG A 42 SHEET 1 B 3 VAL B 83 THR B 90 0 SHEET 2 B 3 LEU B 40 LEU B 46 -1 N VAL B 43 O CYS B 86 SHEET 3 B 3 GLN B 113 LYS B 118 -1 O GLU B 117 N ARG B 42 CISPEP 1 PHE D 1 GLY D 2 0 0.01 CRYST1 27.599 38.320 62.857 90.00 90.10 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 0.036233 0.000000 0.000063 0.00000 SCALE2 0.000000 0.026096 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015909 0.00000