PDB Short entry for 3CX2 HEADER CONTRACTILE PROTEIN 23-APR-08 3CX2 TITLE CRYSTAL STRUCTURE OF THE C1 DOMAIN OF CARDIAC ISOFORM OF MYOSIN TITLE 2 BINDING PROTEIN-C AT 1.3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOSIN-BINDING PROTEIN C, CARDIAC-TYPE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG-LIKE C2-TYPE 1 DOMAIN; 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 GENE: MYBPC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MYOSIN-BINDING PROTEIN; PROTONATION STATES, ACTIN-BINDING, KEYWDS 2 CARDIOMYOPATHY, CELL ADHESION, DISEASE MUTATION, IMMUNOGLOBULIN KEYWDS 3 DOMAIN, MUSCLE PROTEIN, PHOSPHOPROTEIN, POLYMORPHISM, THICK KEYWDS 4 FILAMENT, CONTRACTILE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.FISHER,J.R.HELLIWELL,S.KHURSHID,L.GOVADA,C.REDWOOD,J.M.SQUIRE, AUTHOR 2 N.E.CHAYEN REVDAT 4 30-AUG-23 3CX2 1 REMARK REVDAT 3 25-OCT-17 3CX2 1 SOURCE REMARK REVDAT 2 24-FEB-09 3CX2 1 VERSN REVDAT 1 01-JUL-08 3CX2 0 JRNL AUTH S.J.FISHER,J.R.HELLIWELL,S.KHURSHID,L.GOVADA,C.REDWOOD, JRNL AUTH 2 J.M.SQUIRE,N.E.CHAYEN JRNL TITL AN INVESTIGATION INTO THE PROTONATION STATES OF THE C1 JRNL TITL 2 DOMAIN OF CARDIAC MYOSIN-BINDING PROTEIN C JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 658 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18560154 JRNL DOI 10.1107/S0907444908008792 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R 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) : 0.164 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1184 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 22822 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)) : 0.150 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 876 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 16673 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 843 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 176 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9403 REMARK 3 NUMBER OF RESTRAINTS : 11538 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.027 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) : 0.049 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.058 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.044 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.065 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CX2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000047317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.283 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(III) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26342 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 88.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 33.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2V6H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN AT 20 C USING THE REMARK 280 HANGING DROP METHOD WITH A 2 MICROLITRE DROP CONTAINING A 1:1 REMARK 280 MIXTURE OF PROTEIN SOLUTION AND CRYSTALLISING SOLUTION REMARK 280 CONSISTING OF 8.5% PEG 3350 AND 0.05M HEPES PH 6.8 OVER 500 REMARK 280 MICROLITRES OF CRYSTALLISING SOLUTION IN THE RESERVOIR, PH 6.9, REMARK 280 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: MONOMERIC 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 337 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 SER A 182 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 ASP A 198 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 215 CD - NE - CZ ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG A 215 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 215 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TYR A 220 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 238 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2V6H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C1 DOMAIN OF CARDIAC MYOSIN BINDING REMARK 900 PROTEIN-C DBREF 3CX2 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 *176(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 A 5 GLY A 164 THR A 167 0 SHEET 2 A 5 PHE A 247 HIS A 257 1 O HIS A 257 N VAL A 166 SHEET 3 A 5 GLY A 235 SER A 242 -1 N TYR A 237 O PHE A 252 SHEET 4 A 5 VAL A 188 LYS A 193 -1 N LYS A 190 O GLU A 240 SHEET 5 A 5 VAL A 197 ASP A 198 -1 O VAL A 197 N LYS A 193 SHEET 1 B 3 ILE A 172 ALA A 179 0 SHEET 2 B 3 VAL A 219 ILE A 226 -1 O TYR A 220 N VAL A 178 SHEET 3 B 3 LEU A 207 ASP A 214 -1 N GLN A 208 O 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