PDB Short entry for 3V2R HEADER PROTEIN BINDING 12-DEC-11 3V2R TITLE COMPCC IN COMPLEX WITH FATTY ACIDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARTILAGE OLIGOMERIZATION MATRIX PROTEIN (COILED-COIL COMPND 3 DOMAIN); COMPND 4 CHAIN: A, B, C, D, E; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COMPCC SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS COILED COIL OLEIC ACID, STORAGE, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.STETEFELD REVDAT 2 13-SEP-23 3V2R 1 REMARK REVDAT 1 16-JAN-13 3V2R 0 JRNL AUTH J.STETEFELD JRNL TITL COMPCC IN COMPLEX WITH FATTY ACIDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 661068.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 4761 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.500 REMARK 3 FREE R VALUE TEST SET COUNT : 499 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.015 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 730 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 83 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.045 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.81 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.38 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 54.45 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : OLA.PAR REMARK 3 PARAMETER FILE 7 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : OLA.TOP REMARK 3 TOPOLOGY FILE 7 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3V2R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.25 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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: PDB ENTRY 1MZ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 24.55550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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: 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 ALA A 70 -30.16 -36.70 REMARK 500 ASP B 28 115.91 -24.53 REMARK 500 ALA B 70 64.85 -65.31 REMARK 500 ASP C 69 -80.04 -58.02 REMARK 500 ALA C 70 -53.16 -11.97 REMARK 500 ASP D 28 -119.27 79.32 REMARK 500 GLU D 67 38.13 -76.48 REMARK 500 ASP E 28 -125.83 54.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OLA D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MZ9 RELATED DB: PDB REMARK 900 RELATED ID: 3V2N RELATED DB: PDB REMARK 900 RELATED ID: 3V2Q RELATED DB: PDB REMARK 900 RELATED ID: 3V2P RELATED DB: PDB REMARK 900 RELATED ID: 3V2S RELATED DB: PDB DBREF 3V2R A 27 71 PDB 3V2R 3V2R 27 71 DBREF 3V2R B 27 71 PDB 3V2R 3V2R 27 71 DBREF 3V2R C 27 71 PDB 3V2R 3V2R 27 71 DBREF 3V2R D 27 71 PDB 3V2R 3V2R 27 71 DBREF 3V2R E 27 71 PDB 3V2R 3V2R 27 71 SEQRES 1 A 45 MET ASP LEU ALA PRO GLN MET LEU ARG GLU LEU GLN GLU SEQRES 2 A 45 THR ASN ALA ALA LEU GLN ASP VAL ARG GLU LEU LEU ARG SEQRES 3 A 45 GLN GLN VAL LYS GLU ILE THR PHE LEU LYS ASN THR VAL SEQRES 4 A 45 MET GLU CYS ASP ALA CYS SEQRES 1 B 45 MET ASP LEU ALA PRO GLN MET LEU ARG GLU LEU GLN GLU SEQRES 2 B 45 THR ASN ALA ALA LEU GLN ASP VAL ARG GLU LEU LEU ARG SEQRES 3 B 45 GLN GLN VAL LYS GLU ILE THR PHE LEU LYS ASN THR VAL SEQRES 4 B 45 MET GLU CYS ASP ALA CYS SEQRES 1 C 45 MET ASP LEU ALA PRO GLN MET LEU ARG GLU LEU GLN GLU SEQRES 2 C 45 THR ASN ALA ALA LEU GLN ASP VAL ARG GLU LEU LEU ARG SEQRES 3 C 45 GLN GLN VAL LYS GLU ILE THR PHE LEU LYS ASN THR VAL SEQRES 4 C 45 MET GLU CYS ASP ALA CYS SEQRES 1 D 45 MET ASP LEU ALA PRO GLN MET LEU ARG GLU LEU GLN GLU SEQRES 2 D 45 THR ASN ALA ALA LEU GLN ASP VAL ARG GLU LEU LEU ARG SEQRES 3 D 45 GLN GLN VAL LYS GLU ILE THR PHE LEU LYS ASN THR VAL SEQRES 4 D 45 MET GLU CYS ASP ALA CYS SEQRES 1 E 45 MET ASP LEU ALA PRO GLN MET LEU ARG GLU LEU GLN GLU SEQRES 2 E 45 THR ASN ALA ALA LEU GLN ASP VAL ARG GLU LEU LEU ARG SEQRES 3 E 45 GLN GLN VAL LYS GLU ILE THR PHE LEU LYS ASN THR VAL SEQRES 4 E 45 MET GLU CYS ASP ALA CYS HET OLA D 1 20 HETNAM OLA OLEIC ACID FORMUL 6 OLA C18 H34 O2 FORMUL 7 HOH *54(H2 O) HELIX 1 1 LEU A 29 CYS A 68 1 40 HELIX 2 2 LEU B 29 GLU B 67 1 39 HELIX 3 3 LEU C 29 GLU C 67 1 39 HELIX 4 4 LEU D 29 GLU D 67 1 39 HELIX 5 5 LEU E 29 CYS E 68 1 40 SSBOND 1 CYS A 68 CYS E 71 1555 1555 2.03 SSBOND 2 CYS A 71 CYS B 68 1555 1555 2.03 SSBOND 3 CYS B 71 CYS C 68 1555 1555 2.04 SSBOND 4 CYS C 71 CYS D 68 1555 1555 2.87 SSBOND 5 CYS D 71 CYS E 68 1555 1555 2.03 SITE 1 AC1 14 THR A 40 GLN A 54 LEU B 44 LEU B 51 SITE 2 AC1 14 GLN B 54 GLN C 54 LEU D 37 THR D 40 SITE 3 AC1 14 LEU D 44 LEU D 51 GLN D 54 LEU E 37 SITE 4 AC1 14 THR E 40 GLN E 54 CRYST1 37.862 49.111 54.258 90.00 104.15 90.00 P 1 21 1 10 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 0.026412 0.000000 0.006657 0.00000 SCALE2 0.000000 0.020362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019007 0.00000