HEADER CELL ADHESION 27-JUL-16 5L0I TITLE HUMAN METAVINCULIN MVT R975W CARDIOMYOPATHY-ASSOCIATED MUTANT TITLE 2 (RESIDUES 959-1134) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VINCULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 959-1134; COMPND 5 SYNONYM: METAVINCULIN,MV; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VCL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS 5-HELIX BUNDLE, CYTOSKELETAL PROTEIN, CELL ADHESION, CARDIOMYOPATHY EXPDTA X-RAY DIFFRACTION AUTHOR K.CHINTHALAPUDI,T.IZARD REVDAT 4 04-OCT-23 5L0I 1 REMARK REVDAT 3 23-AUG-17 5L0I 1 JRNL REMARK REVDAT 2 07-SEP-16 5L0I 1 JRNL REVDAT 1 31-AUG-16 5L0I 0 JRNL AUTH K.CHINTHALAPUDI,E.S.RANGARAJAN,D.T.BROWN,T.IZARD JRNL TITL DIFFERENTIAL LIPID BINDING OF VINCULIN ISOFORMS PROMOTES JRNL TITL 2 QUASI-EQUIVALENT DIMERIZATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 9539 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27503891 JRNL DOI 10.1073/PNAS.1600702113 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 5966 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 + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 295 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.74 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.69 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1703 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2037 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1618 REMARK 3 BIN R VALUE (WORKING SET) : 0.2009 REMARK 3 BIN FREE R VALUE : 0.2546 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.99 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 85 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34120 REMARK 3 B22 (A**2) : -7.57440 REMARK 3 B33 (A**2) : 7.23330 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 7.27420 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.281 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 2.924 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.287 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 1.208 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.287 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.882 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1383 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1863 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 518 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 36 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 195 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1383 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 196 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1684 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.03 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.09 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5L0I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 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 : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 44.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 37.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3MYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-CITRATE TRIBASIC DIHYDRATE, REMARK 280 2% TACSIMATE (PH 5), AND 16% PEG 3350, PH 5.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.03700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.75950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.03700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.75950 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 ASN A 959 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN A 1094 O HOH A 2601 2.08 REMARK 500 OE2 GLU A 1089 O HOH A 2602 2.13 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 GOL A 2500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 2501 DBREF 5L0I A 959 1134 UNP P18206 VINC_HUMAN 959 1134 SEQADV 5L0I TRP A 975 UNP P18206 ARG 975 ENGINEERED MUTATION SEQRES 1 A 176 ASN GLN PRO VAL ASN GLN PRO ILE LEU ALA ALA ALA GLN SEQRES 2 A 176 SER LEU HIS TRP GLU ALA THR LYS TRP SER SER LYS GLY SEQRES 3 A 176 ASN ASP ILE ILE ALA ALA ALA LYS ARG MET ALA LEU LEU SEQRES 4 A 176 MET ALA GLU MET SER ARG LEU VAL ARG GLY GLY SER GLY SEQRES 5 A 176 THR LYS ARG ALA LEU ILE GLN CYS ALA LYS ASP ILE ALA SEQRES 6 A 176 LYS ALA SER ASP GLU VAL THR ARG LEU ALA LYS GLU VAL SEQRES 7 A 176 ALA LYS GLN CYS THR ASP LYS ARG ILE ARG THR ASN LEU SEQRES 8 A 176 LEU GLN VAL CYS GLU ARG ILE PRO THR ILE SER THR GLN SEQRES 9 A 176 LEU LYS ILE LEU SER THR VAL LYS ALA THR MET LEU GLY SEQRES 10 A 176 ARG THR ASN ILE SER ASP GLU GLU SER GLU GLN ALA THR SEQRES 11 A 176 GLU MET LEU VAL HIS ASN ALA GLN ASN LEU MET GLN SER SEQRES 12 A 176 VAL LYS GLU THR VAL ARG GLU ALA GLU ALA ALA SER ILE SEQRES 13 A 176 LYS ILE ARG THR ASP ALA GLY PHE THR LEU ARG TRP VAL SEQRES 14 A 176 ARG LYS THR PRO TRP TYR GLN HET GOL A2500 6 HET NA A2501 1 HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 NA NA 1+ FORMUL 4 HOH *66(H2 O) HELIX 1 AA1 ASN A 963 THR A 978 1 16 HELIX 2 AA2 ASN A 985 VAL A 1005 1 21 HELIX 3 AA3 GLY A 1010 CYS A 1040 1 31 HELIX 4 AA4 ASP A 1042 ARG A 1076 1 35 HELIX 5 AA5 SER A 1080 LYS A 1115 1 36 LINK NA NA A2501 O HOH A2619 1555 1555 2.99 SITE 1 AC1 4 SER A 981 SER A 982 LYS A 983 LYS A1129 SITE 1 AC2 2 THR A1130 HOH A2619 CRYST1 90.074 41.519 44.148 90.00 96.14 90.00 C 1 2 1 4 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 0.011102 0.000000 0.001194 0.00000 SCALE2 0.000000 0.024085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022782 0.00000