PDB Short entry for 1GK4 HEADER VIMENTIN 08-AUG-01 1GK4 TITLE HUMAN VIMENTIN COIL 2B FRAGMENT (CYS2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIMENTIN; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: CYS2, RESIDUES 328-411; COMPND 5 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-21D KEYWDS VIMENTIN, INTERMEDIATE FILAMENT, DIMER, PARALLEL COILED KEYWDS 2 COIL, HEPTAD REPEAT, STUTTER EXPDTA X-RAY DIFFRACTION AUTHOR S.V.STRELKOV,H.HERRMANN,N.GEISLER,R.ZIMBELMANN,U.AEBI, AUTHOR 2 P.BURKHARD REVDAT 2 24-FEB-09 1GK4 1 VERSN REVDAT 1 15-MAR-02 1GK4 0 JRNL AUTH S.STRELKOV,H.HERRMANN,N.GEISLER,T.WEDIG, JRNL AUTH 2 R.ZIMBELMANN,U.AEBI,P.BURKHARD JRNL TITL CONSERVED SEGMENTS 1A AND 2B OF THE INTERMEDIATE JRNL TITL 2 FILAMENT DIMER: THEIR ATOMIC STRUCTURES AND ROLE JRNL TITL 3 IN FILAMENT ASSEMBLY. JRNL REF EMBO J. V. 21 1255 2002 JRNL REFN ISSN 0261-4189 JRNL PMID 11889032 JRNL DOI 10.1093/EMBOJ/21.6.1255 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.V.STRELKOV,H.HERRMANN,N.GEISLER,A.LUSTIG, REMARK 1 AUTH 2 S.IVANINSKII,R.ZIMBELMANN,P.BURKHARD,U.AEBI REMARK 1 TITL DIVIDE-AND-CONQUER CRYSTALLOGRAPHIC APPROACH REMARK 1 TITL 2 TOWARDS AN ATOMIC STRUCTURE OF INTERMEDIATE REMARK 1 TITL 3 FILAMENTS REMARK 1 REF J.MOL.BIOL. V. 306 773 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11243787 REMARK 1 DOI 10.1006/JMBI.2001.4442 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.HERRMANN,S.V.STRELKOV,B.FEJA,K.R.ROGERS, REMARK 1 AUTH 2 M.BRETTEL,A.LUSTIG,M.HANER,D.A.D.PARRY, REMARK 1 AUTH 3 P.M.STEINERT,P.BURKHARD,U.AEBI REMARK 1 TITL THE INTERMEDIATE FILAMENT PROTEIN CONSENSUS MOTIF REMARK 1 TITL 2 OF HELIX 2B: ITS ATOMIC STRUCTURE AND CONTRIBUTION REMARK 1 TITL 3 TO ASSEMBLY REMARK 1 REF J.MOL.BIOL. V. 298 817 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10801351 REMARK 1 DOI 10.1006/JMBI.2000.3719 REMARK 2 REMARK 2 RESOLUTION. 2.3 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 34937 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) : 0.242 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.1 REMARK 3 FREE R VALUE TEST SET COUNT : 1095 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1663 REMARK 3 BIN R VALUE (WORKING SET) : 0.349 REMARK 3 BIN FREE R VALUE : 0.313 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.1 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 53 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.043 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3711 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 454 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.63 REMARK 3 B22 (A**2) : 15.06 REMARK 3 B33 (A**2) : -21.69 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.41 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) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.42 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.1 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.7 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.72 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 : 0.328614 REMARK 3 BSOL : 46.2273 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 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1GK4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-01. REMARK 100 THE PDBE ID CODE IS EBI-8053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34937 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.3 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17M NA ACETATE, REMARK 280 25.5% PEG8000, 0.1M CACODYLATE, PH6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.29700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.14150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 120.39250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.29700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.14150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 120.39250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.29700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.14150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 120.39250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.29700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.14150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 120.39250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 HOH A2053 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2054 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2059 LIES ON A SPECIAL POSITION. REMARK 375 HOH C2067 LIES ON A SPECIAL POSITION. REMARK 375 HOH D2076 LIES ON A SPECIAL POSITION. REMARK 375 HOH E2060 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 GLU A 407 REMARK 465 GLU A 408 REMARK 465 SER A 409 REMARK 465 ARG A 410 REMARK 465 ILE A 411 REMARK 465 GLU B 407 REMARK 465 GLU B 408 REMARK 465 SER B 409 REMARK 465 ARG B 410 REMARK 465 ILE B 411 REMARK 465 CYS C 328 REMARK 465 GLU C 329 REMARK 465 VAL C 330 REMARK 465 ASP C 331 REMARK 465 ALA C 332 REMARK 465 LEU C 333 REMARK 465 LYS C 334 REMARK 465 GLY C 335 REMARK 465 THR C 336 REMARK 465 GLU C 407 REMARK 465 GLU C 408 REMARK 465 SER C 409 REMARK 465 ARG C 410 REMARK 465 ILE C 411 REMARK 465 CYS D 328 REMARK 465 GLU D 329 REMARK 465 GLU D 408 REMARK 465 SER D 409 REMARK 465 ARG D 410 REMARK 465 ILE D 411 REMARK 465 CYS E 328 REMARK 465 GLU E 329 REMARK 465 VAL E 330 REMARK 465 ASP E 331 REMARK 465 ALA E 332 REMARK 465 LEU E 333 REMARK 465 LYS E 334 REMARK 465 GLY E 335 REMARK 465 THR E 336 REMARK 465 GLU E 407 REMARK 465 GLU E 408 REMARK 465 SER E 409 REMARK 465 ARG E 410 REMARK 465 ILE E 411 REMARK 465 CYS F 328 REMARK 465 GLU F 329 REMARK 465 VAL F 330 REMARK 465 ASP F 331 REMARK 465 ALA F 332 REMARK 465 GLU F 407 REMARK 465 GLU F 408 REMARK 465 SER F 409 REMARK 465 ARG F 410 REMARK 465 ILE F 411 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 GLU D 407 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 REMARK 500 OE2 GLU A 396 OE2 GLU A 396 4556 2.09 REMARK 500 OD1 ASP C 385 OD1 ASP C 385 3555 2.02 REMARK 500 REMARK 500 REMARK: NULL 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 D 331 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 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 GLU B 329 -11.23 -165.73 REMARK 500 ASP D 331 -61.72 -17.47 REMARK 500 GLU E 338 -75.55 -17.18 REMARK 500 LEU E 404 32.67 -97.60 REMARK 500 THR F 336 22.97 -69.05 REMARK 500 LEU F 404 37.05 -80.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASP D 331 19.8 L L OUTSIDE RANGE 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B1407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GK6 RELATED DB: PDB REMARK 900 HUMAN VIMENTIN COIL 2B FRAGMENT LINKED TO REMARK 900 GCN4 LEUCINE ZIPPER (Z2B) REMARK 900 RELATED ID: 1GK7 RELATED DB: PDB REMARK 900 HUMAN VIMENTIN COIL 1A FRAGMENT (1A) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUE NUMBERING USED IN THE LITERATURE FOR REMARK 999 VIMENTIN DIFFERS BY +1 FROM THE NUMBERING USED REMARK 999 IN SWISSPROT ENTRY P08670 DBREF 1GK4 A 328 411 UNP P08670 VIME_HUMAN 327 410 DBREF 1GK4 B 328 411 UNP P08670 VIME_HUMAN 327 410 DBREF 1GK4 C 328 411 UNP P08670 VIME_HUMAN 327 410 DBREF 1GK4 D 328 411 UNP P08670 VIME_HUMAN 327 410 DBREF 1GK4 E 328 411 UNP P08670 VIME_HUMAN 327 410 DBREF 1GK4 F 328 411 UNP P08670 VIME_HUMAN 327 410 SEQRES 1 A 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 A 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 A 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 A 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 A 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 A 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 A 84 GLY GLU GLU SER ARG ILE SEQRES 1 B 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 B 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 B 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 B 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 B 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 B 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 B 84 GLY GLU GLU SER ARG ILE SEQRES 1 C 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 C 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 C 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 C 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 C 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 C 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 C 84 GLY GLU GLU SER ARG ILE SEQRES 1 D 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 D 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 D 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 D 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 D 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 D 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 D 84 GLY GLU GLU SER ARG ILE SEQRES 1 E 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 E 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 E 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 E 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 E 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 E 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 E 84 GLY GLU GLU SER ARG ILE SEQRES 1 F 84 CYS GLU VAL ASP ALA LEU LYS GLY THR ASN GLU SER LEU SEQRES 2 F 84 GLU ARG GLN MET ARG GLU MET GLU GLU ASN PHE ALA VAL SEQRES 3 F 84 GLU ALA ALA ASN TYR GLN ASP THR ILE GLY ARG LEU GLN SEQRES 4 F 84 ASP GLU ILE GLN ASN MET LYS GLU GLU MET ALA ARG HIS SEQRES 5 F 84 LEU ARG GLU TYR GLN ASP LEU LEU ASN VAL LYS MET ALA SEQRES 6 F 84 LEU ASP ILE GLU ILE ALA THR TYR ARG LYS LEU LEU GLU SEQRES 7 F 84 GLY GLU GLU SER ARG ILE HET ACT B1407 4 HETNAM ACT ACETATE ION FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 HOH *454(H2 O1) HELIX 1 1 CYS A 328 GLU A 405 1 78 HELIX 2 2 VAL B 330 ARG B 401 1 72 HELIX 3 3 SER C 339 GLU C 405 1 67 HELIX 4 4 ALA D 332 LEU D 404 1 73 HELIX 5 5 SER E 339 LEU E 404 1 66 HELIX 6 6 LEU F 333 LEU F 404 1 69 SITE 1 AC1 5 LEU A 380 HIS B 379 GLU B 382 HOH B2064 SITE 2 AC1 5 HOH B2065 CRYST1 76.594 84.283 240.785 90.00 90.00 90.00 I 2 2 2 48 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 0.013056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011865 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004153 0.00000