HEADER PEPTIDE BINDING PROTEIN 22-JUL-10 3O2B TITLE E. COLI CLPS IN COMPLEX WITH A PHE N-END RULE PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 2-106; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHE N-END RULE PEPTIDE; COMPND 8 CHAIN: B, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: CLPS, YLJA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS ADAPTOR, PROTEIN-PEPTIDE COMPLEX, PEPTIDE-BINDING PROTEIN, N-END RULE KEYWDS 2 PEPTIDE, PEPTIDE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.ROMAN-HERNANDEZ,R.A.GRANT,R.T.SAUER,T.A.BAKER,A.DE REGT REVDAT 4 21-FEB-24 3O2B 1 REMARK REVDAT 3 17-JUL-19 3O2B 1 REMARK REVDAT 2 25-APR-12 3O2B 1 REMARK REVDAT 1 14-DEC-11 3O2B 0 JRNL AUTH G.ROMAN-HERNANDEZ,J.Y.HOU,R.A.GRANT,R.T.SAUER,T.A.BAKER JRNL TITL THE CLPS ADAPTOR MEDIATES STAGED DELIVERY OF N-END RULE JRNL TITL 2 SUBSTRATES TO THE AAA+ CLPAP PROTEASE. JRNL REF MOL.CELL V. 43 217 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 21777811 JRNL DOI 10.1016/J.MOLCEL.2011.06.009 REMARK 0 REMARK 0 THIS ENTRY 3O2B REFLECTS AN ALTERNATIVE MODELING OF THE REMARK 0 STRUCTURAL DATA IN 2WA8 ORIGINAL DATA DETERMINED BY AUTHOR: REMARK 0 V.J.SCHUENEMANN,S.M.KRALIK,R.ALBRECHT,S.K.SPALL,K.N.TRUSCOTT, REMARK 0 D.A.DOUGAN,K.ZETH REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 2WA8 REMARK 0 AUTH V.J.SCHUENEMANN,S.M.KRALIK,R.ALBRECHT,S.K.SPALL, REMARK 0 AUTH 2 K.N.TRUSCOTT,D.A.DOUGAN,K.ZETH REMARK 0 TITL STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN REMARK 0 TITL 2 ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS. REMARK 0 REF EMBO REP. V. 10 508 2009 REMARK 0 REFN ISSN 1469-221X REMARK 0 PMID 19373253 REMARK 0 DOI 10.1038/EMBOR.2009.62 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 12294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.010 REMARK 3 FREE R VALUE TEST SET COUNT : 862 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 30.1927 - 3.7234 0.91 1871 142 0.1996 0.2069 REMARK 3 2 3.7234 - 2.9562 0.95 1896 142 0.1697 0.2506 REMARK 3 3 2.9562 - 2.5827 0.95 1922 145 0.2186 0.2443 REMARK 3 4 2.5827 - 2.3467 0.96 1915 145 0.2194 0.2664 REMARK 3 5 2.3467 - 2.1785 0.96 1908 143 0.2459 0.2877 REMARK 3 6 2.1785 - 2.0501 0.96 1920 145 0.2750 0.3182 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 : 0.39 REMARK 3 B_SOL : 54.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.490 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.260 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) : -7.60320 REMARK 3 B22 (A**2) : 6.44800 REMARK 3 B33 (A**2) : -4.44180 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.84500 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 : 0.006 1653 REMARK 3 ANGLE : 1.007 2239 REMARK 3 CHIRALITY : 0.060 253 REMARK 3 PLANARITY : 0.006 286 REMARK 3 DIHEDRAL : 14.855 602 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 3O2B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060575. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13973 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT 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 (%): 37.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M LITHIUM SULFATE, 0.1 M TRIS, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, 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 29.20250 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: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLY A 2 REMARK 465 LYS A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 ASP A 6 REMARK 465 TRP A 7 REMARK 465 LEU A 8 REMARK 465 ASP A 9 REMARK 465 PHE A 10 REMARK 465 ASP A 11 REMARK 465 GLN A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 GLU A 15 REMARK 465 GLU A 16 REMARK 465 LYS A 17 REMARK 465 VAL A 18 REMARK 465 ARG A 19 REMARK 465 ASP A 20 REMARK 465 ALA A 21 REMARK 465 LEU A 22 REMARK 465 GLU D 6 REMARK 465 GLU D 7 REMARK 465 LEU D 8 REMARK 465 PHE D 9 REMARK 465 THR D 10 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 LYS A 23 CG CD CE NZ REMARK 470 LYS B 4 CG CD CE NZ REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 THR C 4 OG1 CG2 REMARK 470 ASN C 5 CG OD1 ND2 REMARK 470 ASP C 6 CG OD1 OD2 REMARK 470 GLN C 12 CG CD OE1 NE2 REMARK 470 LEU C 13 CG CD1 CD2 REMARK 470 LYS C 23 CG CD CE NZ REMARK 470 GLU C 41 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WA8 RELATED DB: PDB REMARK 900 ORIGINAL ENTRY THAT WAS THE SOURCE OF STRUCTURE FACTORS USED IN REMARK 900 REFINEMENT REMARK 900 RELATED ID: 3O2B RELATED DB: PDB REMARK 900 SAME PROTEIN WITH LEU N-END RULE PEPTIDE BOUND REMARK 900 RELATED ID: 3O1F RELATED DB: PDB REMARK 900 SAME PROTEIN WITH NO BOUND PEPTIDE REMARK 900 RELATED ID: 3O2O RELATED DB: PDB DBREF 3O2B A 2 106 UNP P0A8Q6 CLPS_ECOLI 2 106 DBREF 3O2B C 2 106 UNP P0A8Q6 CLPS_ECOLI 2 106 DBREF 3O2B B 1 10 PDB 3O2B 3O2B 1 10 DBREF 3O2B D 1 10 PDB 3O2B 3O2B 1 10 SEQRES 1 A 105 GLY LYS THR ASN ASP TRP LEU ASP PHE ASP GLN LEU ALA SEQRES 2 A 105 GLU GLU LYS VAL ARG ASP ALA LEU LYS PRO PRO SER MET SEQRES 3 A 105 TYR LYS VAL ILE LEU VAL ASN ASP ASP TYR THR PRO MET SEQRES 4 A 105 GLU PHE VAL ILE ASP VAL LEU GLN LYS PHE PHE SER TYR SEQRES 5 A 105 ASP VAL GLU ARG ALA THR GLN LEU MET LEU ALA VAL HIS SEQRES 6 A 105 TYR GLN GLY LYS ALA ILE CYS GLY VAL PHE THR ALA GLU SEQRES 7 A 105 VAL ALA GLU THR LYS VAL ALA MET VAL ASN LYS TYR ALA SEQRES 8 A 105 ARG GLU ASN GLU HIS PRO LEU LEU CYS THR LEU GLU LYS SEQRES 9 A 105 ALA SEQRES 1 B 10 PHE ARG SER LYS GLY GLU GLU LEU PHE THR SEQRES 1 C 105 GLY LYS THR ASN ASP TRP LEU ASP PHE ASP GLN LEU ALA SEQRES 2 C 105 GLU GLU LYS VAL ARG ASP ALA LEU LYS PRO PRO SER MET SEQRES 3 C 105 TYR LYS VAL ILE LEU VAL ASN ASP ASP TYR THR PRO MET SEQRES 4 C 105 GLU PHE VAL ILE ASP VAL LEU GLN LYS PHE PHE SER TYR SEQRES 5 C 105 ASP VAL GLU ARG ALA THR GLN LEU MET LEU ALA VAL HIS SEQRES 6 C 105 TYR GLN GLY LYS ALA ILE CYS GLY VAL PHE THR ALA GLU SEQRES 7 C 105 VAL ALA GLU THR LYS VAL ALA MET VAL ASN LYS TYR ALA SEQRES 8 C 105 ARG GLU ASN GLU HIS PRO LEU LEU CYS THR LEU GLU LYS SEQRES 9 C 105 ALA SEQRES 1 D 10 PHE ARG SER LYS GLY GLU GLU LEU PHE THR HET SO4 A 107 5 HET CL A 1 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 5 SO4 O4 S 2- FORMUL 6 CL CL 1- FORMUL 7 HOH *135(H2 O) HELIX 1 1 PRO A 39 SER A 52 1 14 HELIX 2 2 ASP A 54 GLY A 69 1 16 HELIX 3 3 ALA A 78 ASN A 95 1 18 HELIX 4 4 ASP C 9 LEU C 22 1 14 HELIX 5 5 PRO C 39 SER C 52 1 14 HELIX 6 6 ASP C 54 GLY C 69 1 16 HELIX 7 7 ALA C 78 ASN C 95 1 18 SHEET 1 A 3 LYS A 70 THR A 77 0 SHEET 2 A 3 MET A 27 VAL A 33 -1 N TYR A 28 O PHE A 76 SHEET 3 A 3 LEU A 100 LYS A 105 -1 O GLU A 104 N LYS A 29 SHEET 1 B 3 LYS C 70 THR C 77 0 SHEET 2 B 3 MET C 27 VAL C 33 -1 N TYR C 28 O PHE C 76 SHEET 3 B 3 LEU C 100 LYS C 105 -1 O THR C 102 N ILE C 31 SITE 1 AC1 4 HIS A 66 TYR A 67 GLN A 68 GLY A 69 SITE 1 AC2 2 LYS A 23 ARG A 93 CRYST1 32.223 58.405 56.413 90.00 101.89 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 0.031034 0.000000 0.006534 0.00000 SCALE2 0.000000 0.017122 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018115 0.00000