HEADER HYDROLASE 31-JAN-14 4P15 TITLE STRUCTURE OF THE CLPC N-TERMINAL DOMAIN FROM AN ALKALIPHILIC BACILLUS TITLE 2 LEHENSIS G1 SPECIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACILLUS LEHENSIS CLPC N-TERMINAL DOMAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS LEHENSIS; SOURCE 3 ORGANISM_TAXID: 300825; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HEAT-SHOCK PROTEIN, CLPC, BACILLUS, ALKALOPHILIC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.A.RASHID,D.R.LITTLER,R.M.ILLIAS,A.M.A.MURAD,J.ROSSJOHN,T.BEDDOE, AUTHOR 2 N.M.MAHADI REVDAT 2 27-DEC-23 4P15 1 SOURCE JRNL REMARK REVDAT 1 30-JUL-14 4P15 0 JRNL AUTH S.A.RASHID,D.R.LITTLER JRNL TITL STRUCTURE OF THE CLPC N-TERMINAL DOMAIN AT 1.85 ANGSTROMS JRNL TITL 2 RESOLUTION FROM AN ALKALIPHILIC BACILLUS LEHENSIS G1 SPECIES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.790 REMARK 3 FREE R VALUE TEST SET COUNT : 547 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 36.6486 - 2.9364 1.00 2784 135 0.2005 0.2188 REMARK 3 2 2.9364 - 2.3308 1.00 2718 145 0.2171 0.2441 REMARK 3 3 2.3308 - 2.0362 1.00 2701 144 0.2090 0.2731 REMARK 3 4 2.0362 - 1.8500 0.98 2666 123 0.2470 0.3006 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.820 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 1081 REMARK 3 ANGLE : 0.955 1452 REMARK 3 CHIRALITY : 0.065 166 REMARK 3 PLANARITY : 0.003 188 REMARK 3 DIHEDRAL : 15.646 415 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 4P15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000200109. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 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) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11473 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 73.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 6.850 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 73.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.85 REMARK 200 R MERGE FOR SHELL (I) : 0.05800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 19.60 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: NULL REMARK 200 REMARK 200 REMARK: HEXAGONAL CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CRYSTALLIZATION WAS CARRIED REMARK 280 OUT USING THE HANGING-DROP VAPOR-DIFFUSION METHOD USING 24-WELL REMARK 280 LIMBRO TISSUE CULTURE PLATES (ICN INC.) AT 19C. DROPS WERE REMARK 280 FORMED BY MIXING EQUAL VOLUMES (1 UL) OF PROTEIN SOLUTION AT 50 REMARK 280 MG/ML AND THE RESERVOIR SOLUTION CONTAINING 0.1M PHOSPHATE- REMARK 280 CITRATE PH 4.2 20% POLYETHYLENE GLYCOL 1000, 0.2M LITHIUM REMARK 280 SULPHATE. HEXAGONAL CRYSTALS APPEARED AFTER 20-30 DAYS, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.43333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.71667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.07500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 5.35833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.79167 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 TOTAL BURIED SURFACE AREA: 410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL 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 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 70A REMARK 465 GLN A 70B REMARK 465 GLU A 70C REMARK 465 GLY A 70D REMARK 465 GLN A 70E REMARK 465 LYS A 70F REMARK 465 SER A 70G REMARK 465 ILE A 70H REMARK 465 HIS A 70I 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 DBREF 4P15 A 4 145 PDB 4P15 4P15 4 145 SEQRES 1 A 146 GLY ARG PHE SER GLU ARG ALA GLN LYS VAL LEU ALA LEU SEQRES 2 A 146 SER GLN GLU GLU ALA ILE ARG LEU SER HIS HIS ASN ILE SEQRES 3 A 146 GLY THR GLU HIS ILE LEU LEU GLY LEU ILE ARG GLU GLY SEQRES 4 A 146 GLU GLY ILE ALA ALA LYS ALA LEU GLN GLN LEU GLY LEU SEQRES 5 A 146 GLY SER ASP LYS LEU GLN LYS GLU VAL GLU GLY LEU VAL SEQRES 6 A 146 GLY LYS GLY GLN GLU GLY GLN LYS SER ILE HIS SER THR SEQRES 7 A 146 PRO HIS TYR THR PRO ARG ALA LYS LYS VAL ILE GLU LEU SEQRES 8 A 146 SER MET ASP GLU ALA ARG LYS LEU GLY HIS SER TYR VAL SEQRES 9 A 146 GLY THR GLU HIS ILE LEU LEU GLY LEU ILE ARG GLU GLY SEQRES 10 A 146 GLU GLY VAL ALA ALA ARG VAL LEU ASN ASN LEU GLY VAL SEQRES 11 A 146 SER LEU ASN LYS ALA ARG GLN GLN VAL LEU GLN LEU LEU SEQRES 12 A 146 GLY ASN ASN HET SO4 A 201 5 HET SO4 A 202 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *12(H2 O) HELIX 1 AA1 SER A 7 LEU A 24 1 18 HELIX 2 AA2 GLY A 30 GLY A 42 1 13 HELIX 3 AA3 GLY A 44 LEU A 53 1 10 HELIX 4 AA4 GLY A 56 GLY A 69 1 14 HELIX 5 AA5 THR A 81 LEU A 98 1 18 HELIX 6 AA6 GLY A 104 GLY A 116 1 13 HELIX 7 AA7 GLY A 118 LEU A 127 1 10 HELIX 8 AA8 SER A 130 ASN A 144 1 15 SHEET 1 AA1 2 ASN A 28 ILE A 29 0 SHEET 2 AA1 2 HIS A 79 TYR A 80 1 O HIS A 79 N ILE A 29 SITE 1 AC1 8 GLY A 30 THR A 31 GLU A 32 THR A 81 SITE 2 AC1 8 ARG A 83 GLY A 118 VAL A 119 HOH A 308 SITE 1 AC2 7 SER A 7 ARG A 9 GLY A 44 ILE A 45 SITE 2 AC2 7 GLY A 104 THR A 105 GLU A 106 CRYST1 84.620 84.620 32.150 90.00 90.00 120.00 P 65 6 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 0.011818 0.006823 0.000000 0.00000 SCALE2 0.000000 0.013646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031104 0.00000