PDB Short entry for 2EYN HEADER STRUCTURAL PROTEIN 09-NOV-05 2EYN TITLE CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA-ACTININ 1 TITLE 2 AT 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-ACTININ 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CH DOMAIN (RESIDUES 30-253); COMPND 5 SYNONYM: ALPHA-ACTININ CYTOSKELETAL ISOFORM, NON-MUSCLE ALPHA-ACTININ COMPND 6 1, F-ACTIN CROSS LINKING PROTEIN; COMPND 7 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: ACTN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB12 KEYWDS CALPONIN HOMOLOGY DOMAIN, CH DOMAIN, STRUCTURAL PROTEIN, ACTIN- KEYWDS 2 BINDING, ACTIN-CROSSLINKING, ACTIN-BUNDLING EXPDTA X-RAY DIFFRACTION AUTHOR E.BORREGO-DIAZ,F.KERFF,S.H.LEE,F.FERRON,Y.LI,R.DOMINGUEZ REVDAT 5 23-AUG-23 2EYN 1 SEQADV REVDAT 4 18-OCT-17 2EYN 1 REMARK REVDAT 3 24-FEB-09 2EYN 1 VERSN REVDAT 2 12-SEP-06 2EYN 1 JRNL REVDAT 1 29-AUG-06 2EYN 0 JRNL AUTH E.BORREGO-DIAZ,F.KERFF,S.H.LEE,F.FERRON,Y.LI,R.DOMINGUEZ JRNL TITL CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF JRNL TITL 2 ALPHA-ACTININ 1: EVALUATING TWO COMPETING ACTIN-BINDING JRNL TITL 3 MODELS. JRNL REF J.STRUCT.BIOL. V. 155 230 2006 JRNL REFN ISSN 1047-8477 JRNL PMID 16698282 JRNL DOI 10.1016/J.JSB.2006.01.013 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 16457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT : 967 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1812 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.66300 REMARK 3 B22 (A**2) : -2.12700 REMARK 3 B33 (A**2) : -0.53600 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.280 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 44.59 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPAR:WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2EYN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000035254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17130 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.28300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: HUMAN ALPHA-ACTININ 1 ABD, PDB 2EYI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM NACL, 1MM EDTA, 100MM IMIDAZOL, REMARK 280 24% PEG 5000 MME, PH 6.7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.5K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 26.50350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.53300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.50350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 55.53300 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 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 373 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 81 REMARK 465 ARG A 82 REMARK 465 GLY A 83 REMARK 465 VAL A 108 REMARK 465 SER A 109 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 LYS A 84 CG CD CE NZ REMARK 470 MET A 85 CG SD CE REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 LEU A 107 CG CD1 CD2 REMARK 470 ILE A 110 CG1 CG2 CD1 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 MET A 85 -152.44 -142.49 REMARK 500 LYS A 106 -98.79 -33.79 REMARK 500 ALA A 146 -134.41 57.56 REMARK 500 ASN A 165 82.96 -152.16 REMARK 500 HIS A 170 -100.66 -137.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EYI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ACTIN-BINDING DOMAIN OF HUMAN ALPHA- REMARK 900 ACTININ 1 AT 1.7 ANGSTROM RESOLUTION DBREF 2EYN A 30 253 UNP P12814 ACTN1_HUMAN 30 253 SEQADV 2EYN ALA A 26 UNP P12814 CLONING ARTIFACT SEQADV 2EYN GLY A 27 UNP P12814 CLONING ARTIFACT SEQADV 2EYN HIS A 28 UNP P12814 CLONING ARTIFACT SEQADV 2EYN MET A 29 UNP P12814 CLONING ARTIFACT SEQADV 2EYN GLU A 254 UNP P12814 CLONING ARTIFACT SEQADV 2EYN PHE A 255 UNP P12814 CLONING ARTIFACT SEQADV 2EYN LEU A 256 UNP P12814 CLONING ARTIFACT SEQADV 2EYN GLU A 257 UNP P12814 CLONING ARTIFACT SEQADV 2EYN PRO A 258 UNP P12814 CLONING ARTIFACT SEQADV 2EYN GLY A 259 UNP P12814 CLONING ARTIFACT SEQRES 1 A 234 ALA GLY HIS MET GLU LYS GLN GLN ARG LYS THR PHE THR SEQRES 2 A 234 ALA TRP CYS ASN SER HIS LEU ARG LYS ALA GLY THR GLN SEQRES 3 A 234 ILE GLU ASN ILE GLU GLU ASP PHE ARG ASP GLY LEU LYS SEQRES 4 A 234 LEU MET LEU LEU LEU GLU VAL ILE SER GLY GLU ARG LEU SEQRES 5 A 234 ALA LYS PRO GLU ARG GLY LYS MET ARG VAL HIS LYS ILE SEQRES 6 A 234 SER ASN VAL ASN LYS ALA LEU ASP PHE ILE ALA SER LYS SEQRES 7 A 234 GLY VAL LYS LEU VAL SER ILE GLY ALA GLU GLU ILE VAL SEQRES 8 A 234 ASP GLY ASN VAL LYS MET THR LEU GLY MET ILE TRP THR SEQRES 9 A 234 ILE ILE LEU ARG PHE ALA ILE GLN ASP ILE SER VAL GLU SEQRES 10 A 234 GLU THR SER ALA LYS GLU GLY LEU LEU LEU TRP CYS GLN SEQRES 11 A 234 ARG LYS THR ALA PRO TYR LYS ASN VAL ASN ILE GLN ASN SEQRES 12 A 234 PHE HIS ILE SER TRP LYS ASP GLY LEU GLY PHE CYS ALA SEQRES 13 A 234 LEU ILE HIS ARG HIS ARG PRO GLU LEU ILE ASP TYR GLY SEQRES 14 A 234 LYS LEU ARG LYS ASP ASP PRO LEU THR ASN LEU ASN THR SEQRES 15 A 234 ALA PHE ASP VAL ALA GLU LYS TYR LEU ASP ILE PRO LYS SEQRES 16 A 234 MET LEU ASP ALA GLU ASP ILE VAL GLY THR ALA ARG PRO SEQRES 17 A 234 ASP GLU LYS ALA ILE MET THR TYR VAL SER SER PHE TYR SEQRES 18 A 234 HIS ALA PHE SER GLY ALA GLN GLU PHE LEU GLU PRO GLY FORMUL 2 HOH *156(H2 O) HELIX 1 1 GLY A 27 ARG A 46 1 20 HELIX 2 2 LYS A 47 GLY A 49 5 3 HELIX 3 3 GLY A 62 GLY A 74 1 13 HELIX 4 4 MET A 85 LYS A 103 1 19 HELIX 5 5 GLY A 111 ASP A 117 1 7 HELIX 6 6 ASN A 119 ILE A 136 1 18 HELIX 7 7 ALA A 146 ALA A 159 1 14 HELIX 8 8 HIS A 170 LYS A 174 5 5 HELIX 9 9 GLY A 176 ARG A 187 1 12 HELIX 10 10 PRO A 188 ILE A 191 5 4 HELIX 11 11 ASP A 192 LEU A 196 5 5 HELIX 12 12 ASP A 200 ASP A 217 1 18 HELIX 13 13 ASP A 223 GLY A 229 1 7 HELIX 14 14 ASP A 234 GLY A 251 1 18 HELIX 15 15 GLN A 253 GLU A 257 5 5 SHEET 1 A 2 SER A 140 VAL A 141 0 SHEET 2 A 2 THR A 144 SER A 145 -1 O THR A 144 N VAL A 141 CRYST1 53.007 111.066 31.549 90.00 90.00 90.00 P 21 21 2 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 0.018865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031697 0.00000