HEADER CELL ADHESION 26-APR-07 2YXM TITLE CRYSTAL STRUCTURE OF I-SET DOMAIN OF HUMAN MYOSIN BINDING PROTEINC COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN-BINDING PROTEIN C, SLOW-TYPE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: I-SET DOMAIN; COMPND 5 SYNONYM: SLOW MYBP-C, C-PROTEIN, SKELETAL MUSCLE SLOW ISOFORM; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PK050620-32; SOURCE 7 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS I-SET DOMAIN, MYOSIN BINDING PROTEIN C, CYTOSKELETON, CELL ADHESIONN, KEYWDS 2 STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL KEYWDS 3 AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.KISHISHITA,N.OHSAWA,K.MURAYAMA,L.CHEN,Z.LIU,T.TERADA,M.SHIROUZU, AUTHOR 2 B.WANG,S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 3 13-MAR-24 2YXM 1 SEQADV REVDAT 2 24-FEB-09 2YXM 1 VERSN REVDAT 1 30-OCT-07 2YXM 0 JRNL AUTH S.KISHISHITA,N.OHSAWA,K.MURAYAMA,T.TERADA,L.CHEN,Z.LIU, JRNL AUTH 2 M.SHIROUZU,B.WANG,S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF I-SET DOMAIN OF HUMAN MYOSIN BINDING JRNL TITL 2 PROTEINC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 97006.380 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 15226 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) : 0.196 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 801 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4369 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 225 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 735 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 126 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -0.98000 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) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.680 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 : 0.40 REMARK 3 BSOL : 47.92 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17469 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 26.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 78.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41000 REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M POTTASIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 0.1M TRI-SODIUM CITRATE DIHYDRATE, 2M AMMONIUM REMARK 280 SULFATE, PH 5.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.06700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.59950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.59950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.53350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.59950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.59950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.60050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.59950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.59950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.53350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.59950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.59950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.60050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 35.06700 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 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 BIOMT1 2 0.000000 -1.000000 0.000000 55.19900 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 55.19900 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.06700 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 209 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 210 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 213 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 SER A 2 REMARK 465 SER A 95 REMARK 465 GLY A 96 REMARK 465 PRO A 97 REMARK 465 SER A 98 REMARK 465 SER A 99 REMARK 465 GLY A 100 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 SER A 51 -159.05 -160.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSO002000567.8 RELATED DB: TARGETDB DBREF 2YXM A 8 94 UNP Q00872 MYPC1_HUMAN 252 338 SEQADV 2YXM GLY A 1 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 2 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 3 UNP Q00872 EXPRESSION TAG SEQADV 2YXM GLY A 4 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 5 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 6 UNP Q00872 EXPRESSION TAG SEQADV 2YXM GLY A 7 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 95 UNP Q00872 EXPRESSION TAG SEQADV 2YXM GLY A 96 UNP Q00872 EXPRESSION TAG SEQADV 2YXM PRO A 97 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 98 UNP Q00872 EXPRESSION TAG SEQADV 2YXM SER A 99 UNP Q00872 EXPRESSION TAG SEQADV 2YXM GLY A 100 UNP Q00872 EXPRESSION TAG SEQRES 1 A 100 GLY SER SER GLY SER SER GLY ALA ALA PHE ALA LYS ILE SEQRES 2 A 100 LEU ASP PRO ALA TYR GLN VAL ASP LYS GLY GLY ARG VAL SEQRES 3 A 100 ARG PHE VAL VAL GLU LEU ALA ASP PRO LYS LEU GLU VAL SEQRES 4 A 100 LYS TRP TYR LYS ASN GLY GLN GLU ILE ARG PRO SER THR SEQRES 5 A 100 LYS TYR ILE PHE GLU HIS LYS GLY CYS GLN ARG ILE LEU SEQRES 6 A 100 PHE ILE ASN ASN CYS GLN MET THR ASP ASP SER GLU TYR SEQRES 7 A 100 TYR VAL THR ALA GLY ASP GLU LYS CYS SER THR GLU LEU SEQRES 8 A 100 PHE VAL ARG SER GLY PRO SER SER GLY FORMUL 2 HOH *126(H2 O) HELIX 1 1 SER A 3 ALA A 8 5 6 HELIX 2 2 GLN A 71 ASP A 75 5 5 SHEET 1 A 4 PHE A 10 LYS A 12 0 SHEET 2 A 4 VAL A 26 LEU A 32 -1 O GLU A 31 N ALA A 11 SHEET 3 A 4 GLN A 62 ILE A 67 -1 O LEU A 65 N PHE A 28 SHEET 4 A 4 TYR A 54 LYS A 59 -1 N GLU A 57 O ILE A 64 SHEET 1 B 5 ALA A 17 ASP A 21 0 SHEET 2 B 5 GLU A 85 ARG A 94 1 O ARG A 94 N VAL A 20 SHEET 3 B 5 SER A 76 ALA A 82 -1 N TYR A 78 O THR A 89 SHEET 4 B 5 VAL A 39 LYS A 43 -1 N TYR A 42 O TYR A 79 SHEET 5 B 5 GLN A 46 GLU A 47 -1 O GLN A 46 N LYS A 43 CRYST1 55.199 55.199 70.134 90.00 90.00 90.00 P 41 21 2 8 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 0.018116 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014258 0.00000