HEADER STRUCTURAL PROTEIN 29-FEB-16 5IHN TITLE CRYSTAL STRUCTURE OF THE ALPHA SPECTRIN SH3 DOMAIN MUTANT N47G COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH3 DOMAIN; COMPND 5 SYNONYM: ALPHA-II SPECTRIN,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 GENE: SPTAN1, SPTA2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET26 KEYWDS SH3-LIKE BARREL, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CAMARA-ARTIGAS REVDAT 3 10-JAN-24 5IHN 1 LINK REVDAT 2 13-SEP-17 5IHN 1 REMARK REVDAT 1 29-MAR-17 5IHN 0 JRNL AUTH A.CAMARA-ARTIGAS JRNL TITL CRYSTAL STRUCTURE OF THE ALPHA SPECTRIN SH3 DOMAIN MUTANT JRNL TITL 2 N47G JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 11325 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.8735 - 2.9970 0.97 2415 156 0.1646 0.1792 REMARK 3 2 2.9970 - 2.3801 0.99 2521 126 0.1727 0.1772 REMARK 3 3 2.3801 - 2.0796 0.99 2493 136 0.1400 0.1614 REMARK 3 4 2.0796 - 1.8896 0.99 2520 139 0.1315 0.1623 REMARK 3 5 1.8896 - 1.7543 0.99 2528 102 0.1331 0.1520 REMARK 3 6 1.7543 - 1.6509 1.00 2496 138 0.1609 0.2423 REMARK 3 7 1.6509 - 1.5683 0.99 2511 136 0.1838 0.1901 REMARK 3 8 1.5683 - 1.5000 0.99 2501 136 0.2212 0.2330 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 451 REMARK 3 ANGLE : 0.428 610 REMARK 3 CHIRALITY : 0.045 70 REMARK 3 PLANARITY : 0.004 74 REMARK 3 DIHEDRAL : 8.708 268 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5IHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : CHANNEL-CUT DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR (CINEL), REMARK 200 CRYOCOOLED, 6MM GAP REMARK 200 OPTICS : PAIR OF KB MIRRORS FOR REMARK 200 ADJUSTABLE FOCUSING. UNFOCUSED REMARK 200 BEAM AVAILABLE TOO REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11361 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.870 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.45400 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: PHASER REMARK 200 STARTING MODEL: 3M0R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M SODIUM FORMATE, 0.1 M MES, PH 6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 16.49900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.89150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.93150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.89150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.49900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.93150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 1 REMARK 465 ASP A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 62 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 6 CG CD CE NZ REMARK 470 GLU A 7 CG CD OE1 OE2 REMARK 470 GLN A 16 CG CD OE1 NE2 REMARK 470 LYS A 26 CG CD CE NZ REMARK 470 ASP A 48 CG OD1 OD2 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 102 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 17 OE2 REMARK 620 2 SER A 19 O 130.8 REMARK 620 3 PRO A 20 O 146.8 81.1 REMARK 620 4 GLU A 22 O 86.6 93.8 81.6 REMARK 620 5 TYR A 57 OH 83.9 57.0 114.0 56.7 REMARK 620 6 FMT A 101 O1 84.5 51.0 119.0 68.7 12.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 103 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 55 O REMARK 620 2 VAL A 58 O 83.5 REMARK 620 3 HOH A 236 O 104.0 85.2 REMARK 620 4 HOH A 238 O 91.1 169.0 105.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 103 DBREF 5IHN A 2 62 UNP P07751 SPTN1_CHICK 965 1025 SEQADV 5IHN MET A 1 UNP P07751 INITIATING METHIONINE SEQADV 5IHN GLY A 47 UNP P07751 ASN 1010 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 VAL GLU VAL GLY ASP ARG GLN GLY PHE SEQRES 5 A 62 VAL PRO ALA ALA TYR VAL LYS LYS LEU ASP HET FMT A 101 5 HET NA A 102 1 HET NA A 103 1 HETNAM FMT FORMIC ACID HETNAM NA SODIUM ION FORMUL 2 FMT C H2 O2 FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *42(H2 O) SHEET 1 AA1 5 ARG A 49 PRO A 54 0 SHEET 2 AA1 5 TRP A 41 VAL A 46 -1 N VAL A 44 O GLY A 51 SHEET 3 AA1 5 ILE A 30 ASN A 35 -1 N LEU A 34 O LYS A 43 SHEET 4 AA1 5 GLU A 7 ALA A 11 -1 N GLU A 7 O LEU A 33 SHEET 5 AA1 5 VAL A 58 LYS A 60 -1 O LYS A 59 N LEU A 10 LINK OE2 GLU A 17 NA NA A 102 1555 1555 2.30 LINK O SER A 19 NA NA A 102 1555 1555 2.45 LINK O PRO A 20 NA NA A 102 1555 1555 2.75 LINK O GLU A 22 NA NA A 102 1555 1555 2.38 LINK O ALA A 55 NA NA A 103 1555 1555 2.33 LINK OH TYR A 57 NA NA A 102 1555 4446 2.57 LINK O VAL A 58 NA NA A 103 1555 1555 2.37 LINK O1 FMT A 101 NA NA A 102 1555 4446 2.30 LINK NA NA A 103 O HOH A 236 1555 1555 2.37 LINK NA NA A 103 O HOH A 238 1555 1555 2.50 SITE 1 AC1 7 GLU A 17 PRO A 20 ARG A 49 TYR A 57 SITE 2 AC1 7 NA A 102 HOH A 201 HOH A 206 SITE 1 AC2 6 GLU A 17 SER A 19 PRO A 20 GLU A 22 SITE 2 AC2 6 TYR A 57 FMT A 101 SITE 1 AC3 4 ALA A 55 VAL A 58 HOH A 236 HOH A 238 CRYST1 32.998 41.863 49.783 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 0.030305 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020087 0.00000