HEADER STRUCTURAL PROTEIN 19-MAR-15 4YV3 TITLE TRIMERIC CRYSTAL STRUCTURE OF VIMENTIN COIL1B FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIMENTIN; COMPND 3 CHAIN: A, B, C; COMPND 4 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: VIM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETHSUL KEYWDS CYTOSKELETON, INTERMEDIATE FILAMENT, VIMENTIN, ALPHA-HELICAL COILED- KEYWDS 2 COIL TRIMER, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.A.CHERNYATINA,S.V.STRELKOV REVDAT 3 11-OCT-17 4YV3 1 REMARK REVDAT 2 03-FEB-16 4YV3 1 JRNL REVDAT 1 02-DEC-15 4YV3 0 JRNL AUTH A.A.CHERNYATINA,J.F.HESS,D.GUZENKO,J.C.VOSS,S.V.STRELKOV JRNL TITL HOW TO STUDY INTERMEDIATE FILAMENTS IN ATOMIC DETAIL. JRNL REF METH. ENZYMOL. V. 568 3 2016 JRNL REFN ISSN 1557-7988 JRNL PMID 26795465 JRNL DOI 10.1016/BS.MIE.2015.09.024 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.930 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 1441 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.3918 - 4.3079 0.99 2758 142 0.2344 0.2651 REMARK 3 2 4.3079 - 3.4196 1.00 2816 149 0.2123 0.2482 REMARK 3 3 3.4196 - 2.9874 1.00 2799 153 0.2693 0.3066 REMARK 3 4 2.9874 - 2.7143 1.00 2818 124 0.2710 0.2911 REMARK 3 5 2.7143 - 2.5198 1.00 2829 147 0.2768 0.3680 REMARK 3 6 2.5198 - 2.3712 1.00 2804 120 0.2868 0.3047 REMARK 3 7 2.3712 - 2.2525 1.00 2820 145 0.2875 0.3882 REMARK 3 8 2.2525 - 2.1544 1.00 2762 160 0.2908 0.3243 REMARK 3 9 2.1544 - 2.0715 1.00 2818 156 0.3184 0.3777 REMARK 3 10 2.0715 - 2.0000 0.99 2803 145 0.3390 0.4106 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1889 REMARK 3 ANGLE : 0.487 2534 REMARK 3 CHIRALITY : 0.019 280 REMARK 3 PLANARITY : 0.002 349 REMARK 3 DIHEDRAL : 10.504 791 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4YV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208138. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97895 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29510 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.89500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML PROTEIN IN 10MM TRIS-HCL PH 8, REMARK 280 38 MM NACL MIXED IN V/V RATIO 1:1 WITH AMMONIUM SULPHATE 2.2M, REMARK 280 SODIUM THIOCYANATE 0.2 M, PH 6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 30.47500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 VAL A 161 REMARK 465 VAL B 161 REMARK 465 ASP B 162 REMARK 465 GLN B 163 REMARK 465 VAL C 161 REMARK 465 ASP C 162 REMARK 465 GLN C 163 REMARK 465 LEU C 164 REMARK 465 THR C 165 REMARK 465 ASN C 166 REMARK 465 ASP C 167 REMARK 465 LYS C 168 REMARK 465 ALA C 169 REMARK 465 ARG C 170 REMARK 465 VAL C 171 REMARK 465 GLU C 172 REMARK 465 VAL C 173 REMARK 465 GLU C 174 REMARK 465 ARG C 175 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 NE2 HIS A 238 O2 SO4 A 301 1.79 REMARK 500 NE2 HIS C 238 O2 SO4 A 301 1.93 REMARK 500 OD1 ASP A 162 OG1 THR A 165 2.02 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SWK RELATED DB: PDB REMARK 900 3SWK IS A SIMILAR FRAGMENT TO THE CURRENT PDB ENTRY WITH ADDITIONAL REMARK 900 EIGHT N-TERMINAL RESIDUES, FORMS NATIVE DIMER OF VIMENTIN COIL1B REMARK 900 FRAGMENT REMARK 900 RELATED ID: 4YPC RELATED DB: PDB REMARK 900 4YPC IS A SIMILAR FRAGMENT TO THE CURRENT PDB ENTRY WITH ADDITIONAL REMARK 900 FIVE C-TERMINAL RESIDUES, BOTH FORM UNNATURAL TRIMER OF VIMENTIN REMARK 900 COIL1B FRAGMENT DBREF 4YV3 A 161 238 UNP P08670 VIME_HUMAN 161 238 DBREF 4YV3 B 161 238 UNP P08670 VIME_HUMAN 161 238 DBREF 4YV3 C 161 238 UNP P08670 VIME_HUMAN 161 238 SEQRES 1 A 78 VAL ASP GLN LEU THR ASN ASP LYS ALA ARG VAL GLU VAL SEQRES 2 A 78 GLU ARG ASP ASN LEU ALA GLU ASP ILE MSE ARG LEU ARG SEQRES 3 A 78 GLU LYS LEU GLN GLU GLU MSE LEU GLN ARG GLU GLU ALA SEQRES 4 A 78 GLU ASN THR LEU GLN SER PHE ARG GLN ASP VAL ASP ASN SEQRES 5 A 78 ALA SER LEU ALA ARG LEU ASP LEU GLU ARG LYS VAL GLU SEQRES 6 A 78 SER LEU GLN GLU GLU ILE ALA PHE LEU LYS LYS LEU HIS SEQRES 1 B 78 VAL ASP GLN LEU THR ASN ASP LYS ALA ARG VAL GLU VAL SEQRES 2 B 78 GLU ARG ASP ASN LEU ALA GLU ASP ILE MSE ARG LEU ARG SEQRES 3 B 78 GLU LYS LEU GLN GLU GLU MSE LEU GLN ARG GLU GLU ALA SEQRES 4 B 78 GLU ASN THR LEU GLN SER PHE ARG GLN ASP VAL ASP ASN SEQRES 5 B 78 ALA SER LEU ALA ARG LEU ASP LEU GLU ARG LYS VAL GLU SEQRES 6 B 78 SER LEU GLN GLU GLU ILE ALA PHE LEU LYS LYS LEU HIS SEQRES 1 C 78 VAL ASP GLN LEU THR ASN ASP LYS ALA ARG VAL GLU VAL SEQRES 2 C 78 GLU ARG ASP ASN LEU ALA GLU ASP ILE MSE ARG LEU ARG SEQRES 3 C 78 GLU LYS LEU GLN GLU GLU MSE LEU GLN ARG GLU GLU ALA SEQRES 4 C 78 GLU ASN THR LEU GLN SER PHE ARG GLN ASP VAL ASP ASN SEQRES 5 C 78 ALA SER LEU ALA ARG LEU ASP LEU GLU ARG LYS VAL GLU SEQRES 6 C 78 SER LEU GLN GLU GLU ILE ALA PHE LEU LYS LYS LEU HIS MODRES 4YV3 MSE A 183 MET MODIFIED RESIDUE MODRES 4YV3 MSE A 193 MET MODIFIED RESIDUE MODRES 4YV3 MSE B 183 MET MODIFIED RESIDUE MODRES 4YV3 MSE B 193 MET MODIFIED RESIDUE MODRES 4YV3 MSE C 183 MET MODIFIED RESIDUE MODRES 4YV3 MSE C 193 MET MODIFIED RESIDUE HET MSE A 183 8 HET MSE A 193 8 HET MSE B 183 8 HET MSE B 193 16 HET MSE C 183 8 HET MSE C 193 8 HET SO4 A 301 5 HET CL B 301 1 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 4 SO4 O4 S 2- FORMUL 5 CL CL 1- FORMUL 6 HOH *64(H2 O) HELIX 1 AA1 ASP A 162 HIS A 238 1 77 HELIX 2 AA2 THR B 165 LEU B 237 1 73 HELIX 3 AA3 LEU C 178 LEU C 237 1 60 LINK C ILE A 182 N MSE A 183 1555 1555 1.33 LINK C MSE A 183 N ARG A 184 1555 1555 1.33 LINK C GLU A 192 N MSE A 193 1555 1555 1.33 LINK C MSE A 193 N LEU A 194 1555 1555 1.33 LINK CE1 HIS A 238 O2 SO4 A 301 1555 1555 1.50 LINK C ILE B 182 N MSE B 183 1555 1555 1.33 LINK C MSE B 183 N ARG B 184 1555 1555 1.33 LINK C GLU B 192 N AMSE B 193 1555 1555 1.33 LINK C GLU B 192 N BMSE B 193 1555 1555 1.33 LINK C AMSE B 193 N LEU B 194 1555 1555 1.33 LINK C BMSE B 193 N LEU B 194 1555 1555 1.33 LINK C ILE C 182 N MSE C 183 1555 1555 1.33 LINK C MSE C 183 N ARG C 184 1555 1555 1.33 LINK C GLU C 192 N MSE C 193 1555 1555 1.33 LINK C MSE C 193 N LEU C 194 1555 1555 1.33 SITE 1 AC1 4 HIS A 238 HIS B 238 LEU C 237 HIS C 238 SITE 1 AC2 3 LEU A 220 ARG B 217 ARG C 217 CRYST1 39.060 60.950 48.900 90.00 104.33 90.00 P 1 21 1 6 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 0.025602 0.000000 0.006540 0.00000 SCALE2 0.000000 0.016407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021107 0.00000