PDB Short entry for 1MB8 HEADER STRUCTURAL PROTEIN 02-AUG-02 1MB8 TITLE CRYSTAL STRUCTURE OF THE ACTIN BINDING DOMAIN OF PLECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLECTIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 59-293; COMPND 5 SYNONYM: HD1; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CALPONIN HOMOLOGY DOMAIN, ACTIN BINDING DOMAIN, INTEGRIN KEYWDS 2 BETA4 HEMIDESMOSOMES, CYTOSKELETON, EPIDERMOLYSIS BULLOSA, KEYWDS 3 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.DE PEREDA REVDAT 2 24-FEB-09 1MB8 1 VERSN REVDAT 1 10-JUN-03 1MB8 0 JRNL AUTH B.GARCIA-ALVAREZ,A.BOBKOV,A.SONNENBERG, JRNL AUTH 2 J.M.DE PEREDA JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE ACTIN JRNL TITL 2 BINDING DOMAIN OF PLECTIN SUGGESTS ALTERNATIVE JRNL TITL 3 MECHANISMS FOR BINDING TO F-ACTIN AND INTEGRIN JRNL TITL 4 BETA4 JRNL REF STRUCTURE V. 11 615 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12791251 JRNL DOI 10.1016/S0969-2126(03)00090-X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 11453 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) : 0.212 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 862 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1314 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 109 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2001 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : 0.70000 REMARK 3 B33 (A**2) : 0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.75 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) : 2.860 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.110 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.520 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 48.23 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MB8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-AUG-02. REMARK 100 THE RCSB ID CODE IS RCSB016801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11486 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.79850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.18500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.64150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.18500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.79850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.64150 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 62 CD NE CZ NH1 NH2 REMARK 480 LYS A 143 CG CD CE NZ REMARK 480 VAL A 145 CB CG1 CG2 REMARK 480 ASN A 146 CG OD1 ND2 REMARK 480 SER A 182 OG REMARK 480 GLU A 183 CD OE1 OE2 REMARK 480 GLN A 203 CG CD OE1 NE2 REMARK 480 ARG A 215 NH1 NH2 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 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 ASN A 146 19.69 56.83 REMARK 500 GLU A 183 -35.04 -33.84 REMARK 500 ASN A 209 -171.25 -172.01 REMARK 500 THR A 211 -103.53 -134.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHOR INFORMED THAT THE HWRAE INSERTION HAS BEEN REMARK 999 DESCRIBED IN MOUSE. AUTHOR ALSO INFORMED THAT REMARK 999 RESIDUE ASN 149 IS CORRECT AND THAT THE CONFLICT REMARK 999 ON THIS POSITION IS LIKELY DUE TO POLYMORPHISM. DBREF 1MB8 A 59 293 UNP Q15149 PLEC1_HUMAN 59 293 SEQADV 1MB8 SER A 56 UNP Q15149 CLONING ARTIFACT SEQADV 1MB8 HIS A 57 UNP Q15149 CLONING ARTIFACT SEQADV 1MB8 MET A 58 UNP Q15149 CLONING ARTIFACT SEQADV 1MB8 HIS A 85A UNP Q15149 SEE REMARK 999 SEQADV 1MB8 TRP A 85B UNP Q15149 SEE REMARK 999 SEQADV 1MB8 ARG A 85C UNP Q15149 SEE REMARK 999 SEQADV 1MB8 ALA A 85D UNP Q15149 SEE REMARK 999 SEQADV 1MB8 GLU A 85E UNP Q15149 SEE REMARK 999 SEQADV 1MB8 ASN A 149 UNP Q15149 SEE REMARK 999 SEQRES 1 A 243 SER HIS MET ALA VAL ILE ARG ILE ALA ASP GLU ARG ASP SEQRES 2 A 243 ARG VAL GLN LYS LYS THR PHE THR LYS TRP VAL ASN LYS SEQRES 3 A 243 HIS LEU ILE LYS HIS TRP ARG ALA GLU ALA GLN ARG HIS SEQRES 4 A 243 ILE SER ASP LEU TYR GLU ASP LEU ARG ASP GLY HIS ASN SEQRES 5 A 243 LEU ILE SER LEU LEU GLU VAL LEU SER GLY ASP SER LEU SEQRES 6 A 243 PRO ARG GLU LYS GLY ARG MET ARG PHE HIS LYS LEU GLN SEQRES 7 A 243 ASN VAL GLN ILE ALA LEU ASP TYR LEU ARG HIS ARG GLN SEQRES 8 A 243 VAL LYS LEU VAL ASN ILE ARG ASN ASP ASP ILE ALA ASP SEQRES 9 A 243 GLY ASN PRO LYS LEU THR LEU GLY LEU ILE TRP THR ILE SEQRES 10 A 243 ILE LEU HIS PHE GLN ILE SER ASP ILE GLN VAL SER GLY SEQRES 11 A 243 GLN SER GLU ASP MET THR ALA LYS GLU LYS LEU LEU LEU SEQRES 12 A 243 TRP SER GLN ARG MET VAL GLU GLY TYR GLN GLY LEU ARG SEQRES 13 A 243 CYS ASP ASN PHE THR SER SER TRP ARG ASP GLY ARG LEU SEQRES 14 A 243 PHE ASN ALA ILE ILE HIS ARG HIS LYS PRO LEU LEU ILE SEQRES 15 A 243 ASP MET ASN LYS VAL TYR ARG GLN THR ASN LEU GLU ASN SEQRES 16 A 243 LEU ASP GLN ALA PHE SER VAL ALA GLU ARG ASP LEU GLY SEQRES 17 A 243 VAL THR ARG LEU LEU ASP PRO GLU ASP VAL ASP VAL PRO SEQRES 18 A 243 GLN PRO ASP GLU LYS SER ILE ILE THR TYR VAL SER SER SEQRES 19 A 243 LEU TYR ASP ALA MET PRO ARG VAL PRO FORMUL 2 HOH *153(H2 O) HELIX 1 1 SER A 56 ILE A 84 1 29 HELIX 2 2 ARG A 85C GLN A 87 5 5 HELIX 3 3 GLY A 100 GLY A 112 1 13 HELIX 4 4 MET A 122 ARG A 140 1 19 HELIX 5 5 ARG A 148 ASP A 154 1 7 HELIX 6 6 ASN A 156 ILE A 173 1 18 HELIX 7 7 THR A 186 VAL A 199 1 14 HELIX 8 8 THR A 211 ARG A 215 5 5 HELIX 9 9 GLY A 217 LYS A 228 1 12 HELIX 10 10 PRO A 229 ILE A 232 5 4 HELIX 11 11 ASP A 233 TYR A 238 1 6 HELIX 12 12 THR A 241 GLY A 258 1 18 HELIX 13 13 ASP A 264 ASP A 269 1 6 HELIX 14 14 ASP A 274 MET A 289 1 16 CRYST1 33.597 79.283 82.370 90.00 90.00 90.00 P 21 21 21 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 0.029765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012140 0.00000