HEADER SIGNALING PROTEIN 09-APR-24 9EYC TITLE A-SPECTRIN SH3 DOMAIN V9L, A11V, V23L, M25C, V46W, V53L AND V58L TITLE 2 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, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.VIZARRAGA,I.FITA,D.CIANFERONI,J.DELGADO,L.SERRANO REVDAT 2 13-AUG-25 9EYC 1 JRNL REVDAT 1 06-AUG-25 9EYC 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. 1.06 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) : 1.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35061 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1685 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 28.1900 - 2.4300 1.00 2972 136 0.1791 0.1945 REMARK 3 2 2.4300 - 1.9300 1.00 2843 141 0.1761 0.2290 REMARK 3 3 1.9300 - 1.6800 1.00 2820 129 0.1830 0.1777 REMARK 3 4 1.6800 - 1.5300 1.00 2798 137 0.1938 0.2332 REMARK 3 5 1.5300 - 1.4200 1.00 2731 144 0.2192 0.2380 REMARK 3 6 1.4200 - 1.3400 1.00 2788 135 0.2130 0.2148 REMARK 3 7 1.3400 - 1.2700 1.00 2757 135 0.2218 0.2419 REMARK 3 8 1.2700 - 1.2200 1.00 2734 144 0.2554 0.2701 REMARK 3 9 1.2200 - 1.1700 1.00 2743 152 0.2888 0.3536 REMARK 3 10 1.1700 - 1.1300 1.00 2726 135 0.3373 0.3904 REMARK 3 11 1.1300 - 1.0900 1.00 2737 136 0.3689 0.3804 REMARK 3 12 1.0900 - 1.0600 1.00 2727 161 0.4361 0.4243 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.009 NULL REMARK 3 ANGLE : 1.121 NULL REMARK 3 CHIRALITY : 0.088 79 REMARK 3 PLANARITY : 0.009 98 REMARK 3 DIHEDRAL : 9.076 77 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): 12.6290 11.4379 24.0954 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.1542 REMARK 3 T33: 0.1409 T12: 0.0339 REMARK 3 T13: -0.0066 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 3.1509 L22: 4.0503 REMARK 3 L33: 4.4499 L12: 1.1330 REMARK 3 L13: -0.3710 L23: 0.8679 REMARK 3 S TENSOR REMARK 3 S11: -0.0039 S12: -0.0617 S13: 0.0598 REMARK 3 S21: -0.1178 S22: -0.0119 S23: 0.0690 REMARK 3 S31: -0.0658 S32: -0.1374 S33: 0.0065 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 9EYC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-APR-24. REMARK 100 THE DEPOSITION ID IS D_1292137811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-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 : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.060 REMARK 200 RESOLUTION RANGE LOW (A) : 28.190 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.95300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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 (%): 52.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8M AMMONIUM SULFATE, 0.05 NAI AND REMARK 280 0.1M TRIS PH: 6.5, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 15.59750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.91200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.45600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.91200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.59750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.45600 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: 280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 221 O HOH A 294 2.02 REMARK 500 O HOH A 275 O HOH A 283 2.06 REMARK 500 O ASP A 48 O HOH A 201 2.12 REMARK 500 O HOH A 244 O HOH A 261 2.14 REMARK 500 O HOH A 265 O HOH A 297 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 TRP A 46 117.47 -167.61 REMARK 500 ASN A 47 -128.40 56.77 REMARK 500 ASN A 47 -128.40 51.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 306 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 307 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 308 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 309 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 310 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 311 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 312 DISTANCE = 6.90 ANGSTROMS REMARK 525 HOH A 313 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A 314 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A 315 DISTANCE = 7.05 ANGSTROMS REMARK 525 HOH A 316 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A 317 DISTANCE = 7.33 ANGSTROMS REMARK 525 HOH A 318 DISTANCE = 7.47 ANGSTROMS REMARK 525 HOH A 319 DISTANCE = 7.59 ANGSTROMS DBREF 9EYC A 2 62 UNP P07751 SPTN1_CHICK 965 1025 SEQADV 9EYC MET A 1 UNP P07751 INITIATING METHIONINE SEQADV 9EYC LEU A 9 UNP P07751 VAL 972 ENGINEERED MUTATION SEQADV 9EYC VAL A 11 UNP P07751 ALA 974 ENGINEERED MUTATION SEQADV 9EYC LEU A 23 UNP P07751 VAL 986 ENGINEERED MUTATION SEQADV 9EYC VAL A 25 UNP P07751 MET 988 ENGINEERED MUTATION SEQADV 9EYC TRP A 46 UNP P07751 VAL 1009 ENGINEERED MUTATION SEQADV 9EYC LEU A 53 UNP P07751 VAL 1016 ENGINEERED MUTATION SEQADV 9EYC LEU A 58 UNP P07751 VAL 1021 ENGINEERED MUTATION SEQRES 1 A 62 MET ASP GLU THR GLY LYS GLU LEU LEU 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 TRP ASN ASP ARG GLN GLY PHE SEQRES 5 A 62 LEU PRO ALA ALA TYR LEU LYS LYS LEU ASP HET GOL A 101 9 HET PO4 A 102 5 HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *119(H2 O) SHEET 1 AA1 5 ARG A 49 PRO A 54 0 SHEET 2 AA1 5 TRP A 41 TRP 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 LEU A 8 VAL A 11 -1 N LEU 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 31.195 36.912 65.824 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 0.032056 0.000000 0.000000 0.00000 SCALE2 0.000000 0.027091 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015192 0.00000 CONECT 1113 1114 1115 CONECT 1114 1113 CONECT 1115 1113 1116 1117 CONECT 1116 1115 CONECT 1117 1115 1118 1119 1120 CONECT 1118 1117 1121 CONECT 1119 1117 CONECT 1120 1117 CONECT 1121 1118 CONECT 1122 1123 1124 1125 1126 CONECT 1123 1122 CONECT 1124 1122 CONECT 1125 1122 CONECT 1126 1122 MASTER 289 0 2 0 5 0 0 6 618 1 14 5 END