HEADER CONTRACTILE PROTEIN 07-JUN-04 1TJT TITLE X-RAY STRUCTURE OF THE HUMAN ALPHA-ACTININ ISOFORM 3 AT 2.2A TITLE 2 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-ACTININ 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ACTIN BINDING DOMAIN; COMPND 5 SYNONYM: ALPHA ACTININ SKELETAL MUSCLE ISOFORM 3, F-ACTIN CROSS COMPND 6 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: ACTN3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CALPONIN HOMOLOGY DOMAIN, ACTIN BINDING DOMAIN, CONTRACTILE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.FRANZOT,B.SJOBLOM,M.GAUTEL,K.DJINOVIC CARUGO REVDAT 4 25-OCT-23 1TJT 1 SEQADV REVDAT 3 11-OCT-17 1TJT 1 REMARK REVDAT 2 24-FEB-09 1TJT 1 VERSN REVDAT 1 17-MAY-05 1TJT 0 JRNL AUTH G.FRANZOT,B.SJOBLOM,M.GAUTEL,K.DJINOVIC CARUGO JRNL TITL THE CRYSTAL STRUCTURE OF THE ACTIN BINDING DOMAIN FROM JRNL TITL 2 ALPHA-ACTININ IN ITS CLOSED CONFORMATION: STRUCTURAL INSIGHT JRNL TITL 3 INTO PHOSPHOLIPID REGULATION OF ALPHA-ACTININ JRNL REF J.MOL.BIOL. V. 348 151 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15808860 JRNL DOI 10.1016/J.JMB.2005.01.002 REMARK 2 REMARK 2 RESOLUTION. 2.19 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 867794.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 11674 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) : 0.227 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1197 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1657 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 191 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 3.22000 REMARK 3 B33 (A**2) : -3.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 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) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 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) : 1.970 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.910 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.620 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 53.08 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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : ELLIOTT GX-21 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 : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11674 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 34.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.18600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: AMORE REMARK 200 STARTING MODEL: 1QAG FOR CH1 DOMAIN AND 1BKR FOR CH2 DOMAIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CACODYLATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K 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 19.27000 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 35.25479 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -19.27000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 64.54001 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 SER A 24 REMARK 465 SER A 25 REMARK 465 TYR A 26 REMARK 465 MET A 27 REMARK 465 GLU A 28 REMARK 465 GLN A 29 REMARK 465 GLU A 30 REMARK 465 GLU A 31 REMARK 465 ASP A 32 REMARK 465 TRP A 33 REMARK 465 ASP A 34 REMARK 465 ARG A 35 REMARK 465 ASP A 36 REMARK 465 LEU A 37 REMARK 465 LEU A 38 REMARK 465 LEU A 39 REMARK 465 ASP A 40 REMARK 465 PRO A 41 REMARK 465 ALA A 266 REMARK 465 GLU A 267 REMARK 465 GLN A 268 REMARK 465 ALA A 269 REMARK 465 GLU A 270 REMARK 465 THR A 271 REMARK 465 ALA A 272 REMARK 465 ALA A 273 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 GLU A 67 -61.69 -108.01 REMARK 500 GLU A 71 -50.61 -129.84 REMARK 500 ASP A 72 0.84 -66.25 REMARK 500 LEU A 121 99.99 -60.41 REMARK 500 ALA A 160 -133.68 42.70 REMARK 500 HIS A 184 -87.99 -137.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AOA RELATED DB: PDB REMARK 900 FIMBRIN REMARK 900 RELATED ID: 1DXX RELATED DB: PDB REMARK 900 DYSTROPHIN REMARK 900 RELATED ID: 1MB8 RELATED DB: PDB REMARK 900 PLECTIN REMARK 900 RELATED ID: 1QAG RELATED DB: PDB REMARK 900 UTROPHIN REMARK 900 RELATED ID: 1WKU RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT 1.6 ANGSTROM DBREF 1TJT A 26 273 UNP Q08043 ACTN3_HUMAN 26 273 SEQADV 1TJT SER A 24 UNP Q08043 CLONING ARTIFACT SEQADV 1TJT SER A 25 UNP Q08043 CLONING ARTIFACT SEQRES 1 A 250 SER SER TYR MET GLU GLN GLU GLU ASP TRP ASP ARG ASP SEQRES 2 A 250 LEU LEU LEU ASP PRO ALA TRP GLU LYS GLN GLN ARG LYS SEQRES 3 A 250 THR PHE THR ALA TRP CYS ASN SER HIS LEU ARG LYS ALA SEQRES 4 A 250 GLY THR GLN ILE GLU ASN ILE GLU GLU ASP PHE ARG ASN SEQRES 5 A 250 GLY LEU LYS LEU MET LEU LEU LEU GLU VAL ILE SER GLY SEQRES 6 A 250 GLU ARG LEU PRO ARG PRO ASP LYS GLY LYS MET ARG PHE SEQRES 7 A 250 HIS LYS ILE ALA ASN VAL ASN LYS ALA LEU ASP PHE ILE SEQRES 8 A 250 ALA SER LYS GLY VAL LYS LEU VAL SER ILE GLY ALA GLU SEQRES 9 A 250 GLU ILE VAL ASP GLY ASN LEU LYS MET THR LEU GLY MET SEQRES 10 A 250 ILE TRP THR ILE ILE LEU ARG PHE ALA ILE GLN ASP ILE SEQRES 11 A 250 SER VAL GLU GLU THR SER ALA LYS GLU GLY LEU LEU LEU SEQRES 12 A 250 TRP CYS GLN ARG LYS THR ALA PRO TYR ARG ASN VAL ASN SEQRES 13 A 250 VAL GLN ASN PHE HIS THR SER TRP LYS ASP GLY LEU ALA SEQRES 14 A 250 LEU CYS ALA LEU ILE HIS ARG HIS ARG PRO ASP LEU ILE SEQRES 15 A 250 ASP TYR ALA LYS LEU ARG LYS ASP ASP PRO ILE GLY ASN SEQRES 16 A 250 LEU ASN THR ALA PHE GLU VAL ALA GLU LYS TYR LEU ASP SEQRES 17 A 250 ILE PRO LYS MET LEU ASP ALA GLU ASP ILE VAL ASN THR SEQRES 18 A 250 PRO LYS PRO ASP GLU LYS ALA ILE MET THR TYR VAL SER SEQRES 19 A 250 CYS PHE TYR HIS ALA PHE ALA GLY ALA GLU GLN ALA GLU SEQRES 20 A 250 THR ALA ALA FORMUL 2 HOH *193(H2 O) HELIX 1 1 ALA A 42 ARG A 60 1 19 HELIX 2 2 LYS A 61 GLY A 63 5 3 HELIX 3 3 GLY A 76 GLY A 88 1 13 HELIX 4 4 MET A 99 SER A 116 1 18 HELIX 5 5 GLY A 125 ASP A 131 1 7 HELIX 6 6 ASN A 133 ILE A 150 1 18 HELIX 7 7 ALA A 160 ALA A 173 1 14 HELIX 8 8 HIS A 184 LYS A 188 5 5 HELIX 9 9 GLY A 190 ARG A 201 1 12 HELIX 10 10 ASP A 206 LEU A 210 5 5 HELIX 11 11 ASP A 214 LEU A 230 1 17 HELIX 12 12 ASP A 237 THR A 244 1 8 HELIX 13 13 ASP A 248 GLY A 265 1 18 SHEET 1 A 2 SER A 154 VAL A 155 0 SHEET 2 A 2 THR A 158 SER A 159 -1 O THR A 158 N VAL A 155 CRYST1 46.310 38.540 65.480 90.00 99.72 90.00 P 1 21 1 2 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 0.021594 0.000000 0.003699 0.00000 SCALE2 0.000000 0.025947 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015494 0.00000