PDB Short entry for 1TUD HEADER CYTOSKELETON 29-FEB-96 1TUD TITLE ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT N47- TITLE 2 D48 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-SPECTRIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SRC HOMOLOGY 3 DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: THIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN COMPND 8 SH3 SEQUENCE (PDB CODE WT-3D STRUCTURE: 1SGB). THE RESIDUE NUMBERS COMPND 9 ARE AS IN THE WT SPECTRIN-SH3 DOMAIN (1SGB). THR 4 (N-TERMINUS) AND COMPND 10 ASP 62 (C-TERMINUS) OF THE WT-SH3 SEQUENCE ARE LINKED BY TWO COMPND 11 ADDITIONAL RESIDUES (SER 2, GLY 3). THE CHAIN IS CLEAVED BETWEEN ASN COMPND 12 47 AND ASP 48. MET 0 IS ADDED AT THE NEW N-TERMINUS. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS CAPPING PROTEIN, CALCIUM-BINDING, DUPLICATION, SH3 DOMAIN, KEYWDS 2 CYTOSKELETON EXPDTA X-RAY DIFFRACTION AUTHOR A.R.VIGUERA,L.SERRANO,M.WILMANNS REVDAT 4 14-FEB-24 1TUD 1 REMARK REVDAT 3 03-NOV-21 1TUD 1 SEQADV REVDAT 2 24-FEB-09 1TUD 1 VERSN REVDAT 1 01-AUG-96 1TUD 0 JRNL AUTH A.R.VIGUERA,F.J.BLANCO,L.SERRANO JRNL TITL THE ORDER OF SECONDARY STRUCTURE ELEMENTS DOES NOT DETERMINE JRNL TITL 2 THE STRUCTURE OF A PROTEIN BUT DOES AFFECT ITS FOLDING JRNL TITL 3 KINETICS. JRNL REF J.MOL.BIOL. V. 247 670 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7723022 JRNL DOI 10.1006/JMBI.1994.0171 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6467 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 485 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.49 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 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.447 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.143 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FIRST TWO RESIDUES OF REMARK 3 THE NEW N-TERMINUS (MET 0, ASP 48) ARE NOT VISIBLE REMARK 3 IN THE ELECTRON DENSITY MAP. REMARK 4 REMARK 4 1TUD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUN-95 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6591 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 2.640 REMARK 200 R MERGE (I) : 0.04300 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 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 15.97500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.09500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.09500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.97500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.44000 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 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 MET A 47A REMARK 465 ASP A 48 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 90 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS A CIRCULAR PERMUTANT OF THE WT ALPHA-SPECTRIN REMARK 999 SH3 SEQUENCE (PDB CODE WT-3D STRUCTURE: 1SGB). THE REMARK 999 RESIDUE NUMBERS ARE AS IN THE WT SPECTRIN-SH3 DOMAIN REMARK 999 (1SGB). THR 4 (N-TERMINUS) AND ASP 62 (C-TERMINUS) OF REMARK 999 THE WT-SH3 SEQUENCE ARE LINKED BY TWO ADDITIONAL RESIDUES REMARK 999 (SER 2, GLY 3). THE CHAIN IS CLEAVED BETWEEN ASN 47 AND REMARK 999 ASP 48. MET 0 IS ADDED AT THE NEW N-TERMINUS. DBREF 1TUD A 50 47 UNP P07751 SPTA2_CHICK 952 1010 SEQADV 1TUD GLY A 51 UNP P07751 ALA 953 CONFLICT SEQADV 1TUD PHE A 52 UNP P07751 GLN 954 CONFLICT SEQADV 1TUD VAL A 53 UNP P07751 SER 955 CONFLICT SEQADV 1TUD PRO A 54 UNP P07751 CYS 956 CONFLICT SEQADV 1TUD ALA A 55 UNP P07751 ARG 957 CONFLICT SEQADV 1TUD ALA A 56 UNP P07751 GLN 958 CONFLICT SEQADV 1TUD TYR A 57 UNP P07751 GLN 959 CONFLICT SEQADV 1TUD LYS A 59 UNP P07751 ALA 961 CONFLICT SEQADV 1TUD LYS A 60 UNP P07751 PRO 962 CONFLICT SEQADV 1TUD LEU A 61 UNP P07751 THR 963 CONFLICT SEQADV 1TUD SER A 2 UNP P07751 ASP 965 ENGINEERED MUTATION SEQADV 1TUD GLY A 3 UNP P07751 GLU 966 ENGINEERED MUTATION SEQRES 1 A 62 MET ASP ARG GLN GLY PHE VAL PRO ALA ALA TYR VAL LYS SEQRES 2 A 62 LYS LEU ASP SER GLY THR GLY LYS GLU LEU VAL LEU ALA SEQRES 3 A 62 LEU TYR ASP TYR GLN GLU LYS SER PRO ARG GLU VAL THR SEQRES 4 A 62 MET LYS LYS GLY ASP ILE LEU THR LEU LEU ASN SER THR SEQRES 5 A 62 ASN LYS ASP TRP TRP LYS VAL GLU VAL ASN FORMUL 2 HOH *57(H2 O) HELIX 1 1 ALA A 55 TYR A 57 5 3 SHEET 1 A 5 GLN A 50 PRO A 54 0 SHEET 2 A 5 TRP A 41 GLU A 45 -1 N VAL A 44 O GLY A 51 SHEET 3 A 5 ILE A 30 ASN A 35 -1 N ASN A 35 O LYS A 43 SHEET 4 A 5 LEU A 8 ALA A 11 -1 N VAL A 9 O LEU A 31 SHEET 5 A 5 VAL A 58 LYS A 60 -1 N LYS A 59 O LEU A 10 CRYST1 31.950 42.880 54.190 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 0.031299 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023321 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018454 0.00000