HEADER PROTEIN BINDING 07-OCT-02 1MZ9 TITLE STORAGE FUNCTION OF COMP:THE CRYSTAL STRUCTURE OF THE COILED-COIL TITLE 2 DOMAIN IN COMPLEX WITH VITAMIN D3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARTILAGE OLIGOMERIC MATRIX PROTEIN; COMPND 3 CHAIN: A, B, C, D, E; COMPND 4 FRAGMENT: RESIDUES 27-71; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JM109-DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3B KEYWDS PENTAMERIC COILED-COIL DOMAIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.STETEFELD REVDAT 3 21-DEC-22 1MZ9 1 REMARK SEQADV REVDAT 2 24-FEB-09 1MZ9 1 VERSN REVDAT 1 28-JAN-03 1MZ9 0 JRNL AUTH S.OZBEK,J.ENGEL,J.STETEFELD JRNL TITL STORAGE FUNCTION OF CARTILAGE OLIGOMERIC MATRIX PROTEIN: THE JRNL TITL 2 CRYSTAL STRUCTURE OF THE COILED-COIL DOMAIN IN COMPLEX WITH JRNL TITL 3 VITAMIN D(3). JRNL REF EMBO J. V. 21 5960 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 12426368 JRNL DOI 10.1093/EMBOJ/CDF628 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 950772.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21621 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) : 0.231 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2162 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3240 REMARK 3 BIN R VALUE (WORKING SET) : 0.3080 REMARK 3 BIN FREE R VALUE : 0.3520 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 347 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 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 : 58 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.37000 REMARK 3 B22 (A**2) : -4.21000 REMARK 3 B33 (A**2) : 1.85000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.83000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 15.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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 : 0.39 REMARK 3 BSOL : 71.02 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 : F_CHAIRB.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017323. 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 : 10 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22133 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 24.64450 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: 13390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11050 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLU D 67 REMARK 475 CYS D 68 REMARK 475 ASP D 69 REMARK 475 ALA D 70 REMARK 475 CYS D 71 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 ASP D 28 -114.10 64.97 REMARK 500 ASP E 28 173.77 57.27 REMARK 500 LEU E 29 28.72 -73.55 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 VDY D 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VDY A 1002 DBREF 1MZ9 A 28 71 UNP Q9R0G6 COMP_MOUSE 28 71 DBREF 1MZ9 B 28 71 UNP Q9R0G6 COMP_MOUSE 28 71 DBREF 1MZ9 C 28 71 UNP Q9R0G6 COMP_MOUSE 28 71 DBREF 1MZ9 D 28 71 UNP Q9R0G6 COMP_MOUSE 28 71 DBREF 1MZ9 E 28 71 UNP Q9R0G6 COMP_MOUSE 28 71 SEQADV 1MZ9 MET A 27 UNP Q9R0G6 INITIATING METHIONINE SEQADV 1MZ9 MET B 27 UNP Q9R0G6 INITIATING METHIONINE SEQADV 1MZ9 MET C 27 UNP Q9R0G6 INITIATING METHIONINE SEQADV 1MZ9 MET D 27 UNP Q9R0G6 INITIATING METHIONINE SEQADV 1MZ9 MET E 27 UNP Q9R0G6 INITIATING METHIONINE 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 VDY A1002 29 HET VDY D1001 29 HETNAM VDY 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL- HETNAM 2 VDY OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE- HETNAM 3 VDY CYCLOHEXANOL HETSYN VDY 25-HYDROXYVITAMIN D3 FORMUL 6 VDY 2(C27 H44 O2) FORMUL 8 HOH *245(H2 O) HELIX 1 1 LEU A 29 GLU A 67 1 39 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 GLU E 67 1 39 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 2.03 SSBOND 4 CYS D 71 CYS E 68 1555 1555 2.03 SITE 1 AC1 12 THR A 40 LEU A 51 LEU B 44 VAL B 47 SITE 2 AC1 12 LEU B 51 LEU C 44 LEU C 51 THR D 40 SITE 3 AC1 12 LEU D 44 VAL D 47 LEU D 51 LEU E 44 SITE 1 AC2 16 ILE A 58 LEU A 61 ALA A 70 ILE B 58 SITE 2 AC2 16 LEU B 61 VAL B 65 ILE C 58 LEU C 61 SITE 3 AC2 16 VAL C 65 ALA C 70 LEU D 61 VAL D 65 SITE 4 AC2 16 LEU E 61 VAL E 65 CYS E 68 ALA E 70 CRYST1 38.295 49.289 55.260 90.00 103.87 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 0.026113 0.000000 0.006447 0.00000 SCALE2 0.000000 0.020289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018640 0.00000