HEADER PEPTIDE BINDING PROTEIN 02-FEB-09 3G3P TITLE THE STRUCTURE OF THE M53A MUTANT OF THE CAULOBACTER CRESCENTUS CLPS IN TITLE 2 COMPLEX WITH A PEPTIDE CONTAINING AN AMINO-TERMINAL NORLEUCINE TITLE 3 RESIDUE 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 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEPTIDE (NLE)LFVQRDSKE; COMPND 8 CHAIN: D; COMPND 9 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SYNTHETIC PEPTIDE CONTAINING UNNATURAL AMINO ACID SOURCE 14 NORLEUCINE AT IT'S AMINO TERMINUS 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 3 20-OCT-21 3G3P 1 REMARK SEQADV LINK REVDAT 2 01-NOV-17 3G3P 1 REMARK REVDAT 1 09-MAR-10 3G3P 0 JRNL AUTH G.ROMAN-HERNANDEZ,R.A.GRANT,R.T.SAUER,T.A.BAKER JRNL TITL STRUCTURE OF CAULOBACTER CRESCENTUS CLPS IN COMPLEX WITH JRNL TITL 2 VARIOUS PEPTIDES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.4_129 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 3 NUMBER OF REFLECTIONS : 22463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1126 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 20.9044 - 2.9538 0.97 2961 163 0.1647 0.1847 REMARK 3 2 2.9538 - 2.3455 0.98 2946 156 0.1487 0.1678 REMARK 3 3 2.3455 - 2.0493 0.97 2892 168 0.1406 0.1791 REMARK 3 4 2.0493 - 1.8621 0.96 2836 148 0.1534 0.2061 REMARK 3 5 1.8621 - 1.7287 0.95 2846 150 0.1600 0.1877 REMARK 3 6 1.7287 - 1.6268 0.94 2789 134 0.1522 0.1772 REMARK 3 7 1.6268 - 1.5454 0.85 2546 136 0.1446 0.1823 REMARK 3 8 1.5454 - 1.4781 0.51 1521 71 0.1462 0.1423 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 : 0.45 REMARK 3 B_SOL : 33.22 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.120 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.83000 REMARK 3 B22 (A**2) : -8.79800 REMARK 3 B33 (A**2) : -8.50800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.56600 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 1455 REMARK 3 ANGLE : 0.825 1986 REMARK 3 CHIRALITY : 0.044 224 REMARK 3 PLANARITY : 0.003 258 REMARK 3 DIHEDRAL : 16.461 550 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 3G3P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000051383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX-HF REMARK 200 OPTICS : VARIMAX-HR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 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 (%) : 89.3 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.5230 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.06800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 0.2 M MGCL2, 13% PEG REMARK 280 3350, PH 5.5, 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 27.02450 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, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 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: 3 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: 510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 PHE D 3 REMARK 465 VAL D 4 REMARK 465 GLN D 5 REMARK 465 ARG D 6 REMARK 465 ASP D 7 REMARK 465 SER D 8 REMARK 465 LYS D 9 REMARK 465 GLU D 10 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 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 119 O REMARK 620 2 HOH A 146 O 91.3 REMARK 620 3 HOH A 204 O 81.4 86.9 REMARK 620 4 ASP B 119 O 83.5 174.5 90.5 REMARK 620 5 HOH B 144 O 91.0 100.9 169.3 81.1 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3G1B RELATED DB: PDB REMARK 900 SAME PROTEIN - DIFFERENT PEPTIDE DBREF 3G3P A 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 DBREF 3G3P B 35 119 UNP Q9A5I0 CLPS_CAUCR 35 119 DBREF 3G3P D 1 10 PDB 3G3P 3G3P 1 10 SEQADV 3G3P ALA A 53 UNP Q9A5I0 MET 53 ENGINEERED MUTATION SEQADV 3G3P ALA B 53 UNP Q9A5I0 MET 53 ENGINEERED MUTATION 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 ALA 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 ALA 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 D 10 NLE LEU PHE VAL GLN ARG ASP SER LYS GLU MODRES 3G3P NLE D 1 LEU NORLEUCINE HET NLE D 1 21 HET MG A 1 1 HETNAM NLE NORLEUCINE HETNAM MG MAGNESIUM ION FORMUL 3 NLE C6 H13 N O2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *307(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 PHE B 64 1 13 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 VAL A 43 O CYS A 86 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 VAL B 43 O CYS B 86 SHEET 3 B 3 GLN B 113 LYS B 118 -1 O THR B 115 N LEU B 44 LINK C NLE D 1 N LEU D 2 1555 1555 1.33 LINK MG MG A 1 O ASP A 119 1555 1555 2.21 LINK MG MG A 1 O HOH A 146 1555 1555 2.54 LINK MG MG A 1 O HOH A 204 1555 1555 2.70 LINK MG MG A 1 O ASP B 119 1555 1555 2.19 LINK MG MG A 1 O HOH B 144 1555 1555 2.57 SITE 1 AC1 6 ASP A 119 HOH A 146 HOH A 204 ASP B 119 SITE 2 AC1 6 HOH B 144 HOH B 199 CRYST1 33.665 54.049 44.615 90.00 110.44 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 0.029704 0.000000 0.011071 0.00000 SCALE2 0.000000 0.018502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023920 0.00000