HEADER STRUCTURAL PROTEIN 20-FEB-25 9IH6 TITLE A-SPECTRIN SH3 DOMAIN V9Y, A11V, V23L, M25V, V53L, V58L MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPECTRIN ALPHA CHAIN, NON-ERYTHROCYTIC 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-II SPECTRIN,FODRIN ALPHA CHAIN; COMPND 5 ENGINEERED: YES; COMPND 6 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 KEYWDS THREE-DIMENSIONAL STRUCTURE, SH3 DOMAIN, CELL SIGNALING, SRC-FAMILY, KEYWDS 2 HYDROPHOBIC-CORE MUTATIONS, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.VIZARRAGA,I.FITA,D.CIANFERONI,J.DELGADO,L.SERRANO REVDAT 2 13-AUG-25 9IH6 1 JRNL REVDAT 1 06-AUG-25 9IH6 0 JRNL AUTH D.CIANFERONI,D.VIZARRAGA,A.M.FERNANDEZ-ESCAMILLA,I.FITA, JRNL AUTH 2 R.HAMDANI,R.RECHE,J.DELGADO,L.SERRANO JRNL TITL ARTIFICIAL INTELLIGENCE AND FIRST-PRINCIPLE METHODS IN JRNL TITL 2 PROTEIN REDESIGN: A MARRIAGE OF CONVENIENCE? JRNL REF PROTEIN SCI. V. 34 70210 2025 JRNL REFN ESSN 1469-896X JRNL PMID 40671352 JRNL DOI 10.1002/PRO.70210 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15814 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 789 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 41.8600 - 2.3800 1.00 2646 131 0.1847 0.2300 REMARK 3 2 2.3800 - 1.8900 1.00 2528 124 0.1849 0.1966 REMARK 3 3 1.8900 - 1.6500 1.00 2477 141 0.1872 0.2094 REMARK 3 4 1.6500 - 1.5000 1.00 2478 127 0.1947 0.2092 REMARK 3 5 1.5000 - 1.3900 1.00 2441 136 0.2288 0.2659 REMARK 3 6 1.3900 - 1.3100 1.00 2455 130 0.3078 0.3565 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.50 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.7454 11.6254 1.7367 REMARK 3 T TENSOR REMARK 3 T11: 0.1705 T22: 0.1503 REMARK 3 T33: 0.1526 T12: -0.0098 REMARK 3 T13: -0.0030 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.4631 L22: 0.4005 REMARK 3 L33: 0.7294 L12: 0.4106 REMARK 3 L13: -0.1598 L23: 0.0163 REMARK 3 S TENSOR REMARK 3 S11: 0.0069 S12: 0.0528 S13: -0.0181 REMARK 3 S21: 0.0409 S22: -0.0396 S23: -0.0386 REMARK 3 S31: 0.1540 S32: -0.0718 S33: -0.0000 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 9IH6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292145654. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 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) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15822 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.309 REMARK 200 RESOLUTION RANGE LOW (A) : 41.864 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.92500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 1M NA/K TARTRATE REMARK 280 AND 0.1M SODIUM CITRATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 12.53050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 12.53050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.30350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.86350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.30350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.86350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 12.53050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.30350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.86350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 12.53050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.30350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.86350 REMARK 290 SMTRY3 8 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 CZ ARG A 49 LIES ON A SPECIAL POSITION. 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 ASP A 2 -70.24 -35.61 REMARK 500 SER A 36 79.09 -151.08 REMARK 500 ASN A 47 64.04 39.39 REMARK 500 ASN A 47 -124.06 46.78 REMARK 500 REMARK 500 REMARK: NULL DBREF 9IH6 A 2 62 UNP P07751 SPTN1_CHICK 965 1025 SEQADV 9IH6 MET A 1 UNP P07751 INITIATING METHIONINE SEQADV 9IH6 TYR A 9 UNP P07751 VAL 972 ENGINEERED MUTATION SEQADV 9IH6 VAL A 11 UNP P07751 ALA 974 ENGINEERED MUTATION SEQADV 9IH6 LEU A 23 UNP P07751 VAL 986 ENGINEERED MUTATION SEQADV 9IH6 VAL A 25 UNP P07751 MET 988 ENGINEERED MUTATION SEQADV 9IH6 LEU A 53 UNP P07751 VAL 1016 ENGINEERED MUTATION SEQADV 9IH6 LEU A 58 UNP P07751 VAL 1021 ENGINEERED MUTATION SEQRES 1 A 62 MET ASP GLU THR GLY LYS GLU LEU TYR LEU VAL LEU TYR SEQRES 2 A 62 ASP TYR GLN GLU LYS SER PRO ARG GLU LEU THR VAL 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 ASN ASP ARG GLN GLY PHE SEQRES 5 A 62 LEU PRO ALA ALA TYR LEU LYS LYS LEU ASP HET GOL A 101 6 HET GOL A 102 6 HET GOL A 103 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *41(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 ASN A 35 O LYS A 43 SHEET 4 AA1 5 LEU A 8 VAL A 11 -1 N TYR A 9 O LEU A 31 SHEET 5 AA1 5 LEU A 58 LYS A 60 -1 O LYS A 59 N LEU A 10 CRYST1 60.607 83.727 25.061 90.00 90.00 90.00 C 2 2 21 8 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 0.016500 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039903 0.00000 CONECT 648 649 650 CONECT 649 648 CONECT 650 648 651 652 CONECT 651 650 CONECT 652 650 653 CONECT 653 652 CONECT 654 655 656 CONECT 655 654 CONECT 656 654 657 658 CONECT 657 656 CONECT 658 656 659 CONECT 659 658 CONECT 660 661 662 CONECT 661 660 CONECT 662 660 663 664 CONECT 663 662 CONECT 664 662 665 CONECT 665 664 MASTER 253 0 3 0 5 0 0 6 575 1 18 5 END