HEADER HYDROLASE 21-JUL-10 3O1F TITLE P1 CRYSTAL FORM OF E. COLI CLPS AT 1.4 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 26-106; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 26-106; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CLPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 GENE: CLPS; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADAPTOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.ROMAN-HERNANDEZ,J.Y.HOU,R.A.GRANT,R.T.SAUER,T.A.BAKER REVDAT 3 08-NOV-17 3O1F 1 REMARK REVDAT 2 17-AUG-11 3O1F 1 JRNL REVDAT 1 27-JUL-11 3O1F 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 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 3 NUMBER OF REFLECTIONS : 23635 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1173 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 22.4905 - 2.7986 0.90 3072 149 0.1522 0.1687 REMARK 3 2 2.7986 - 2.2220 0.95 3224 174 0.1479 0.1783 REMARK 3 3 2.2220 - 1.9413 0.93 3164 140 0.1490 0.1719 REMARK 3 4 1.9413 - 1.7639 0.90 3064 176 0.1724 0.1932 REMARK 3 5 1.7639 - 1.6375 0.89 3044 157 0.1765 0.1976 REMARK 3 6 1.6375 - 1.5410 0.87 2980 168 0.1795 0.2001 REMARK 3 7 1.5410 - 1.4638 0.79 2699 134 0.1876 0.2619 REMARK 3 8 1.4638 - 1.4001 0.36 1215 75 0.2167 0.2104 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 42.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.12540 REMARK 3 B22 (A**2) : -2.36160 REMARK 3 B33 (A**2) : -4.76380 REMARK 3 B12 (A**2) : -1.15720 REMARK 3 B13 (A**2) : -0.85870 REMARK 3 B23 (A**2) : 3.40850 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 : 0.007 1340 REMARK 3 ANGLE : 1.194 1815 REMARK 3 CHIRALITY : 0.070 210 REMARK 3 PLANARITY : 0.009 229 REMARK 3 DIHEDRAL : 17.242 486 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 3O1F 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_1000060543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX-HR 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 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23654 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.4 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 32.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.15000 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 (%): 39.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM FORMATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, HANGING DROP, PH 7, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 119 O HOH B 245 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 3O1F A 26 106 UNP D3QP81 D3QP81_ECOCB 26 106 DBREF 3O1F B 26 106 UNP D3QP81 D3QP81_ECOCB 26 106 SEQRES 1 A 81 SER MET TYR LYS VAL ILE LEU VAL ASN ASP ASP TYR THR SEQRES 2 A 81 PRO MET GLU PHE VAL ILE ASP VAL LEU GLN LYS PHE PHE SEQRES 3 A 81 SER TYR ASP VAL GLU ARG ALA THR GLN LEU MET LEU ALA SEQRES 4 A 81 VAL HIS TYR GLN GLY LYS ALA ILE CYS GLY VAL PHE THR SEQRES 5 A 81 ALA GLU VAL ALA GLU THR LYS VAL ALA SME VAL ASN LYS SEQRES 6 A 81 TYR ALA ARG GLU ASN GLU HIS PRO LEU LEU CYS THR LEU SEQRES 7 A 81 GLU LYS ALA SEQRES 1 B 81 SER MET TYR LYS VAL ILE LEU VAL ASN ASP ASP TYR THR SEQRES 2 B 81 PRO MET GLU PHE VAL ILE ASP VAL LEU GLN LYS PHE PHE SEQRES 3 B 81 SER TYR ASP VAL GLU ARG ALA THR GLN LEU MET LEU ALA SEQRES 4 B 81 VAL HIS TYR GLN GLY LYS ALA ILE CYS GLY VAL PHE THR SEQRES 5 B 81 ALA GLU VAL ALA GLU THR LYS VAL ALA MET VAL ASN LYS SEQRES 6 B 81 TYR ALA ARG GLU ASN GLU HIS PRO LEU LEU CYS THR LEU SEQRES 7 B 81 GLU LYS ALA MODRES 3O1F SME A 87 MET METHIONINE SULFOXIDE HET SME A 87 18 HETNAM SME METHIONINE SULFOXIDE FORMUL 1 SME C5 H11 N O3 S FORMUL 3 HOH *402(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 THR A 77 ASN A 95 1 19 HELIX 4 4 PRO B 39 SER B 52 1 14 HELIX 5 5 ASP B 54 GLY B 69 1 16 HELIX 6 6 ALA B 78 ASN B 95 1 18 SHEET 1 A 3 LYS A 70 PHE A 76 0 SHEET 2 A 3 TYR A 28 VAL A 33 -1 N VAL A 30 O CYS A 73 SHEET 3 A 3 LEU A 100 LYS A 105 -1 O THR A 102 N ILE A 31 SHEET 1 B 3 LYS B 70 THR B 77 0 SHEET 2 B 3 MET B 27 VAL B 33 -1 N VAL B 30 O CYS B 73 SHEET 3 B 3 LEU B 100 LYS B 105 -1 O THR B 102 N ILE B 31 LINK C ALA A 86 N SME A 87 1555 1555 1.33 LINK C SME A 87 N VAL A 88 1555 1555 1.33 CRYST1 28.025 28.051 51.624 80.50 77.88 72.30 P 1 1 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 0.035682 -0.011390 -0.006466 0.00000 SCALE2 0.000000 0.037422 -0.004092 0.00000 SCALE3 0.000000 0.000000 0.019931 0.00000