PDB Short entry for 2V6H HEADER CELL ADHESION 18-JUL-07 2V6H TITLE CRYSTAL STRUCTURE OF THE C1 DOMAIN OF CARDIAC MYOSIN BINDING PROTEIN-C COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN-BINDING PROTEIN C, CARDIAC-TYPE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C1 DOMAIN, RESIDUES 151-258; COMPND 5 SYNONYM: CARDIAC MYBP-C, C-PROTEIN, CARDIAC MUSCLE 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 ORGAN: HEART; SOURCE 6 TISSUE: CARDIAC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS CELL ADHESION, PHOSPHORYLATION, MYBP-C C1 DOMAIN, DISEASE MUTATION, KEYWDS 2 MUSCLE REGULATION, IGI DOMAIN STRUCTURE, MUSCLE PROTEIN, KEYWDS 3 CARDIOMYOPATHY, THICK FILAMENT, IMMUNOGLOBULIN DOMAIN, HYPERTROPIC KEYWDS 4 CARDIOMYOPATHY, POLYMORPHISM, ACTIN-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR L.GOVATA,L.CARPENTER,P.C.A.DA FONSECA,J.R.HELLIWELL,P.J.RIZKALLAH, AUTHOR 2 E.FLASHMAN,N.E.CHAYEN,C.REDWOOD,J.M.SQUIRE REVDAT 4 08-MAY-19 2V6H 1 REMARK REVDAT 3 23-AUG-17 2V6H 1 JRNL REMARK REVDAT 2 24-FEB-09 2V6H 1 VERSN REVDAT 1 22-JUL-08 2V6H 0 JRNL AUTH L.GOVADA,L.CARPENTER,P.C.DA FONSECA,J.R.HELLIWELL, JRNL AUTH 2 P.RIZKALLAH,E.FLASHMAN,N.E.CHAYEN,C.REDWOOD,J.M.SQUIRE JRNL TITL CRYSTAL STRUCTURE OF THE C1 DOMAIN OF CARDIAC MYOSIN BINDING JRNL TITL 2 PROTEIN-C: IMPLICATIONS FOR HYPERTROPHIC CARDIOMYOPATHY. JRNL REF J. MOL. BIOL. V. 378 387 2008 JRNL REFN ESSN 1089-8638 JRNL PMID 18374358 JRNL DOI 10.1016/J.JMB.2008.02.044 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.184 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 652 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 12687 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.177 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 584 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 11471 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 985.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4050 REMARK 3 NUMBER OF RESTRAINTS : 3548 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.042 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.048 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.006 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.047 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS SOLVED USING THREE - REMARK 3 WAVELENGTH MAD DATA AT SRS 10.1 TO A RESOLUTION LIMIT OF REMARK 3 2.4ANGSTROM. THE DATA FOR REFINEMENT IS AS DETAILED MEASURED ON REMARK 3 SRS 14.1. THE PROTEIN COORDINATES OVERALL 'CRUICKSHANK REMARK 3 DIFFRACTION PRECISION INDICATOR (DPI)' 0.0982 ANGSTROM (BASED ON REMARK 3 RFACTOR) AND 0.1074 ANGSTROM (BASED ON THE RFREE). REMARK 4 REMARK 4 2V6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290033222. 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 : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MONO AND MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16401 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.8 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE, CNS, REFMAC, SHELXL-97 REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP; 20 C; 18%PEG, 0.1M REMARK 280 BUFFER, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 24.42400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 24.42400 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.56600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.42400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.78300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.42400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 71.34900 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.42400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.42400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.56600 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 24.42400 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 71.34900 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 24.42400 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 23.78300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.1 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 48.84800 REMARK 350 BIOMT3 2 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 A1082 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 ALA A 181 REMARK 465 SER A 182 REMARK 465 LEU A 183 REMARK 465 LEU A 184 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 185 CG CD CE NZ REMARK 470 LYS A 244 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 160 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 238 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1136 DISTANCE = 6.56 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GXE RELATED DB: PDB REMARK 900 CENTRAL DOMAIN OF CARDIAC MYOSIN BINDING PROTEIN C REMARK 900 RELATED ID: 1PD6 RELATED DB: PDB REMARK 900 THE NMR STRUCTURE OF DOMAIN C2 OF HUMAN CARDIAC MYOSINBINDING REMARK 900 PROTEIN C REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE C1 DOMAIN IS A 105 AMINO ACIDS PORTION. DBREF 2V6H A 151 258 UNP Q14896 MYPC3_HUMAN 151 258 SEQRES 1 A 108 ASP ASP PRO ILE GLY LEU PHE VAL MET ARG PRO GLN ASP SEQRES 2 A 108 GLY GLU VAL THR VAL GLY GLY SER ILE THR PHE SER ALA SEQRES 3 A 108 ARG VAL ALA GLY ALA SER LEU LEU LYS PRO PRO VAL VAL SEQRES 4 A 108 LYS TRP PHE LYS GLY LYS TRP VAL ASP LEU SER SER LYS SEQRES 5 A 108 VAL GLY GLN HIS LEU GLN LEU HIS ASP SER TYR ASP ARG SEQRES 6 A 108 ALA SER LYS VAL TYR LEU PHE GLU LEU HIS ILE THR ASP SEQRES 7 A 108 ALA GLN PRO ALA PHE THR GLY SER TYR ARG CYS GLU VAL SEQRES 8 A 108 SER THR LYS ASP LYS PHE ASP CYS SER ASN PHE ASN LEU SEQRES 9 A 108 THR VAL HIS GLU FORMUL 2 HOH *170(H2 O) HELIX 1 1 SER A 200 VAL A 203 5 4 HELIX 2 2 GLN A 230 THR A 234 5 5 SHEET 1 AA 5 GLY A 164 THR A 167 0 SHEET 2 AA 5 PHE A 247 HIS A 257 1 O ASN A 253 N GLY A 164 SHEET 3 AA 5 GLY A 235 SER A 242 -1 O GLY A 235 N LEU A 254 SHEET 4 AA 5 VAL A 188 LYS A 193 -1 O VAL A 188 N SER A 242 SHEET 5 AA 5 VAL A 197 ASP A 198 -1 O VAL A 197 N LYS A 193 SHEET 1 AB 3 ILE A 172 ALA A 179 0 SHEET 2 AB 3 VAL A 219 ILE A 226 -1 O TYR A 220 N VAL A 178 SHEET 3 AB 3 LEU A 207 ASP A 214 -1 O GLN A 208 N HIS A 225 CRYST1 48.848 48.848 95.132 90.00 90.00 90.00 I 41 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 0.020472 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010512 0.00000