HEADER SIGNALING PROTEIN 09-APR-24 9EYF TITLE A-SPECTRIN SH3 DOMAIN V9L, A11V, V23L, M25L, V46Y, V53I 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 9EYF 1 JRNL REVDAT 1 06-AUG-25 9EYF 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. 1.34 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 11530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 539 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 31.2500 - 2.1300 1.00 2881 132 0.1958 0.2353 REMARK 3 2 2.1300 - 1.6900 1.00 2754 127 0.2364 0.2535 REMARK 3 3 1.6900 - 1.4800 1.00 2699 134 0.2512 0.2941 REMARK 3 4 1.4800 - 1.3400 1.00 2657 146 0.2936 0.3291 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) : 33.870 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 : 0.007 NULL REMARK 3 ANGLE : 0.992 NULL REMARK 3 CHIRALITY : 0.086 76 REMARK 3 PLANARITY : 0.007 83 REMARK 3 DIHEDRAL : 12.126 64 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 9EYF 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_1292137814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.8 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) : 0.97926 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 : 11534 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 31.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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 FOR SHELL : 1.000 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 (%): 26.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M AMMONIUM SULFATE AND 0.1M TRIS REMARK 280 PH: 6.7, PH 6.8, VAPOR DIFFUSION, HANGING DROP, 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 12.31450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.24700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.02350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.24700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.31450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.02350 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 PRO A 20 REMARK 465 ARG A 21 REMARK 465 GLU A 22 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 132 O HOH A 134 2.14 REMARK 500 REMARK 500 REMARK: NULL DBREF 9EYF A 2 62 UNP P07751 SPTN1_CHICK 965 1025 SEQADV 9EYF MET A 1 UNP P07751 INITIATING METHIONINE SEQADV 9EYF LEU A 9 UNP P07751 VAL 972 ENGINEERED MUTATION SEQADV 9EYF VAL A 11 UNP P07751 ALA 974 ENGINEERED MUTATION SEQADV 9EYF LEU A 23 UNP P07751 VAL 986 ENGINEERED MUTATION SEQADV 9EYF LEU A 25 UNP P07751 MET 988 ENGINEERED MUTATION SEQADV 9EYF TYR A 46 UNP P07751 VAL 1009 ENGINEERED MUTATION SEQADV 9EYF ILE A 53 UNP P07751 VAL 1016 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 LEU 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 TYR ASN ASP ARG GLN GLY PHE SEQRES 5 A 62 ILE PRO ALA ALA TYR VAL LYS LYS LEU ASP FORMUL 2 HOH *34(H2 O) SHEET 1 AA1 5 ARG A 49 PRO A 54 0 SHEET 2 AA1 5 TRP A 41 TYR 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 VAL A 58 LYS A 60 -1 O LYS A 59 N LEU A 10 SHEET 1 AA2 2 TYR A 15 GLN A 16 0 SHEET 2 AA2 2 THR A 24 LEU A 25 -1 O LEU A 25 N TYR A 15 CRYST1 24.629 32.047 62.494 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 0.040603 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031204 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016002 0.00000 ANISOU 143 N GLU A 17 7377 6580 6452 1072 -337 572 N ANISOU 144 CA GLU A 17 8412 7085 6800 1150 -426 567 C ANISOU 145 C GLU A 17 8741 7444 7203 1418 -421 913 C ANISOU 146 O GLU A 17 8659 7373 7206 1560 -470 1059 O ANISOU 147 CB GLU A 17 9122 7113 6735 1146 -608 223 C ANISOU 148 CG GLU A 17 9800 7183 6705 1190 -1002 -107 C ANISOU 149 CD GLU A 17 10326 7263 6745 1062 -1321 -324 C ANISOU 150 OE1 GLU A 17 10349 7172 6735 1044 -1522 -450 O ANISOU 151 OE2 GLU A 17 10468 7430 6795 877 -1409 -366 O ANISOU 152 N LYS A 18 9146 8025 7561 1453 -360 1092 N ANISOU 153 CA LYS A 18 9545 8526 7894 1379 -144 1255 C ANISOU 154 C LYS A 18 9641 8808 8092 1243 72 1369 C ANISOU 155 O LYS A 18 9628 8944 8143 1215 130 1366 O ANISOU 156 CB LYS A 18 9718 8806 8005 1405 -133 1237 C ANISOU 157 CG LYS A 18 9883 8990 8110 1371 -189 1193 C ANISOU 158 CD LYS A 18 10051 9166 8202 1395 -170 1144 C ANISOU 159 CE LYS A 18 10169 9337 8259 1348 -123 1116 C ANISOU 160 NZ LYS A 18 10152 9386 8283 1266 -163 1086 N ANISOU 161 N SER A 19 9836 9010 8255 1158 159 1457 N ANISOU 162 CA SER A 19 10058 9108 8435 1069 265 1497 C ANISOU 163 C SER A 19 10047 8998 8528 1059 389 1532 C ANISOU 164 O SER A 19 10002 9020 8580 1050 491 1574 O ANISOU 165 CB SER A 19 10217 9285 8503 998 320 1507 C ANISOU 166 OG SER A 19 10349 9353 8542 941 310 1602 O TER 500 ASP A 62 HETATM 501 O HOH A 101 2.407 1.935 16.752 1.00 54.78 O HETATM 502 O HOH A 102 -10.775 5.007 8.463 1.00 48.76 O HETATM 503 O HOH A 103 -11.928 1.937 2.950 1.00 39.84 O HETATM 504 O HOH A 104 -14.362 -13.170 6.452 1.00 27.30 O HETATM 505 O HOH A 105 3.517 -9.659 12.061 1.00 57.06 O HETATM 506 O HOH A 106 5.645 0.613 -1.228 1.00 32.77 O HETATM 507 O HOH A 107 5.382 11.016 10.928 1.00 54.29 O HETATM 508 O HOH A 108 -4.477 -11.513 1.362 1.00 40.09 O HETATM 509 O HOH A 109 -2.620 4.111 -3.227 1.00 43.45 O HETATM 510 O HOH A 110 -1.057 11.248 14.501 1.00 22.02 O HETATM 511 O HOH A 111 -4.025 -12.166 -1.456 1.00 20.90 O HETATM 512 O HOH A 112 -15.951 -9.589 10.715 1.00 42.02 O HETATM 513 O HOH A 113 9.678 -10.222 13.726 1.00 37.69 O HETATM 514 O HOH A 114 1.729 -7.665 -4.556 1.00 19.36 O HETATM 515 O HOH A 115 -2.723 -10.069 16.121 1.00 49.85 O HETATM 516 O HOH A 116 -10.262 -4.722 14.080 1.00 24.93 O HETATM 517 O HOH A 117 -2.252 -1.835 19.685 1.00 33.67 O HETATM 518 O HOH A 118 -5.560 -2.329 -5.723 1.00 31.77 O HETATM 519 O HOH A 119 3.746 5.354 12.574 1.00 34.87 O HETATM 520 O HOH A 120 -7.884 7.364 8.513 1.00 36.69 O HETATM 521 O HOH A 121 -9.797 9.038 4.893 1.00 41.98 O HETATM 522 O HOH A 122 8.519 -6.020 15.625 1.00 43.31 O HETATM 523 O HOH A 123 -3.528 1.185 -8.140 1.00 50.63 O HETATM 524 O HOH A 124 -4.464 -11.127 6.257 1.00 35.33 O HETATM 525 O HOH A 125 -5.968 7.422 18.436 1.00 35.78 O HETATM 526 O HOH A 126 5.299 3.989 9.935 1.00 44.71 O HETATM 527 O HOH A 127 14.603 0.073 17.641 1.00 50.13 O HETATM 528 O HOH A 128 6.202 3.426 23.202 1.00 46.13 O HETATM 529 O HOH A 129 -13.610 2.329 4.315 1.00 38.28 O HETATM 530 O HOH A 130 -8.886 8.455 2.960 1.00 52.62 O HETATM 531 O HOH A 131 -2.056 -12.490 7.670 1.00 26.99 O HETATM 532 O HOH A 132 -11.844 -2.081 -0.462 1.00 28.02 O HETATM 533 O HOH A 133 -14.832 -1.440 1.020 1.00 35.21 O HETATM 534 O HOH A 134 -12.410 -0.459 0.819 1.00 50.11 O MASTER 214 0 0 0 7 0 0 6 525 1 0 5 END