HEADER SH3-DOMAIN 18-DEC-03 1UUE TITLE A-SPECTRIN SH3 DOMAIN (V44T, D48G MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN, RESIDUES 965-1025; COMPND 5 SYNONYM: SPECTRIN NON-ERYTHROID ALPHA CHAIN, FODRIN ALPHA CHAIN; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 TISSUE: MUSCLE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PBAT4 KEYWDS SH3-DOMAIN, SH3, SPECTRIN, CYTOSKELETON, MEMBRANE, CALMODULIN- KEYWDS 2 BINDING, ACTIN-BINDING, CALCIUM-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.C.VEGA,A.FERNANDEZ,M.WILMANNS,L.SERRANO REVDAT 7 13-DEC-23 1UUE 1 REMARK REVDAT 6 16-OCT-19 1UUE 1 REMARK REVDAT 5 24-JUL-19 1UUE 1 REMARK REVDAT 4 10-JUL-19 1UUE 1 REMARK REVDAT 3 24-OCT-18 1UUE 1 SOURCE REMARK REVDAT 2 24-FEB-09 1UUE 1 VERSN REVDAT 1 19-FEB-04 1UUE 0 JRNL AUTH A.FERNANDEZ,M.C.VEGA,M.WILMANNS,L.SERRANO JRNL TITL SOLVATION IN PROTEIN FOLDING ANALYSIS: COMBINATION OF JRNL TITL 2 THEORETICAL AND EXPERIMENTAL APPROACHES JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 2834 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14978284 JRNL DOI 10.1073/PNAS.0304180101 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.MUSSACCHIO,M.NOBLE,R.PAUPTIT,R.WIERENGA,M.SARASTE REMARK 1 TITL CRYSTAL STRUCTURE OF A SRC-HOMOLOGY 3 (SH3) DOMAIN REMARK 1 REF NATURE V. 359 851 1992 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 1279434 REMARK 1 DOI 10.1038/359851A0 REMARK 2 REMARK 2 RESOLUTION. 2.60 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 2184 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) : 0.240 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 106 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.026 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 345 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 17 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.082 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.51000 REMARK 3 B22 (A**2) : -0.70000 REMARK 3 B33 (A**2) : -1.81000 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.36 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) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.46 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 7.800 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 10.480; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 9.380 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.690; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: NULL REMARK 4 REMARK 4 1UUE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1290014243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.802 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2184 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.08300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 26.30 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: PDB ENTRY 1BK2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, SITTING DROP 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 16.54700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.80800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.93850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.80800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.54700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.93850 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION VAL 1007 THR, ASP 1011 GLY 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 1 REMARK 465 ASP A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 GLY A 5 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 TYR A 15 114.83 -166.56 REMARK 500 ASN A 47 74.31 13.94 REMARK 500 LEU A 61 75.03 -110.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AEY RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, SOLUTION NMR, 15 STRUCTURES REMARK 900 RELATED ID: 1AJ3 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE SPECTRIN REPEAT, NMR, 20 STRUCTURES REMARK 900 RELATED ID: 1BK2 RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN D48G MUTANT REMARK 900 RELATED ID: 1CUN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF REPEATS 16 AND 17 OF CHICKEN BRAIN ALPHA REMARK 900 SPECTRIN REMARK 900 RELATED ID: 1E6G RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN D48G MUTANT REMARK 900 RELATED ID: 1E6H RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN A11V, M25I, V44I, V58L MUTANTS REMARK 900 RELATED ID: 1E7O RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V44I, V58L MUTATIONS REMARK 900 RELATED ID: 1G2B RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT,CUT AT N47- REMARK 900 D48 REMARK 900 RELATED ID: 1H8K RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN A11V, V23L, M25V, V53I, V58L MUTANT REMARK 900 RELATED ID: 1HD3 RELATED DB: PDB REMARK 900 A-SPECTRIN SH3 DOMAIN F52Y MUTANT REMARK 900 RELATED ID: 1M8M RELATED DB: PDB REMARK 900 SOLID-STATE MAS NMR STRUCTURE OF THE A- SPECTRIN SH3 DOMAIN REMARK 900 RELATED ID: 1NEG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF N-AND C- TERMINAL LABELED SH3-DOMAIN REMARK 900 OF ALPHA-CHICKEN SPECTRIN REMARK 900 RELATED ID: 1PWT RELATED DB: PDB REMARK 900 THERMODYNAMIC ANALYSIS OF ALPHA-SPECTRIN SH3 AND TWO OF ITSCIRCULAR REMARK 900 PERMUTANTS WITH DIFFERENT LOOP LENGTHS: DISCERNINGTHE REASONS FOR REMARK 900 RAPID FOLDING IN PROTEINS REMARK 900 RELATED ID: 1QKW RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, N47G MUTANT IN THE DISTAL REMARK 900 LOOP. REMARK 900 RELATED ID: 1QKX RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, N47A MUTANT IN THE DISTAL REMARK 900 LOOP. REMARK 900 RELATED ID: 1SHG RELATED DB: PDB REMARK 900 ALPHA SPECTRIN (SH3 DOMAIN) REMARK 900 RELATED ID: 1TUC RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT REMARK 900 S19-P20 REMARK 900 RELATED ID: 1TUD RELATED DB: PDB REMARK 900 ALPHA-SPECTRIN SRC HOMOLOGY 3 DOMAIN, CIRCULAR PERMUTANT, CUT AT REMARK 900 N47-D48 DBREF 1UUE A 1 1 PDB 1UUE 1UUE 1 1 DBREF 1UUE A 2 62 UNP P07751 SPCN_CHICK 965 1025 SEQADV 1UUE THR A 44 UNP P07751 VAL 1007 ENGINEERED MUTATION SEQADV 1UUE GLY A 48 UNP P07751 ASP 1011 ENGINEERED MUTATION SEQRES 1 A 62 MET ASP GLU THR GLY LYS GLU LEU VAL LEU ALA LEU TYR SEQRES 2 A 62 ASP TYR GLN GLU LYS SER PRO ARG GLU VAL THR MET LYS SEQRES 3 A 62 LYS GLY ASP ILE LEU THR LEU LEU ASN SER THR ASN LYS SEQRES 4 A 62 ASP TRP TRP LYS THR GLU VAL ASN GLY ARG GLN GLY PHE SEQRES 5 A 62 VAL PRO ALA ALA TYR VAL LYS LYS LEU ASP FORMUL 2 HOH *24(H2 O) SHEET 1 AA 5 ARG A 49 PRO A 54 0 SHEET 2 AA 5 TRP A 41 VAL A 46 -1 O TRP A 42 N VAL A 53 SHEET 3 AA 5 ILE A 30 ASN A 35 -1 O THR A 32 N GLU A 45 SHEET 4 AA 5 LEU A 8 ALA A 11 -1 O VAL A 9 N LEU A 31 SHEET 5 AA 5 VAL A 58 LYS A 60 -1 O LYS A 59 N LEU A 10 CRYST1 33.094 41.877 49.616 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 0.030217 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020155 0.00000