HEADER PROTEIN BINDING 05-NOV-18 6IPY TITLE HIS-TAGGED FYN SH3 DOMAIN R96I MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE FYN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 82-144; COMPND 5 EC: 2.7.10.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: FYN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS KINASE, SH3 DOMAIN, HEXA-HISTIDINE TAG, CRYSTAL STABILIZED BY KEYWDS 2 HISTIDINE TAG, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.T.AROLD,S.S.ALJEDANI,U.F.SHAHUL HAMEED REVDAT 3 22-NOV-23 6IPY 1 REMARK REVDAT 2 20-OCT-21 6IPY 1 JRNL REVDAT 1 28-NOV-18 6IPY 0 JRNL AUTH A.ALDEHAIMAN,A.A.MOMIN,A.RESTOUIN,L.WANG,X.SHI,S.ALJEDANI, JRNL AUTH 2 S.OPI,A.LUGARI,U.F.SHAHUL HAMEED,L.PONCHON,X.MORELLI, JRNL AUTH 3 M.HUANG,C.DUMAS,Y.COLLETTE,S.T.AROLD JRNL TITL SYNERGY AND ALLOSTERY IN LIGAND BINDING BY HIV-1 NEF. JRNL REF BIOCHEM.J. V. 478 1525 2021 JRNL REFN ESSN 1470-8728 JRNL PMID 33787846 JRNL DOI 10.1042/BCJ20201002 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 12373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 617 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 41.5399 - 2.1298 1.00 3043 161 0.1604 0.1894 REMARK 3 2 2.1298 - 1.6905 1.00 2973 156 0.2104 0.2068 REMARK 3 3 1.6905 - 1.4768 1.00 2954 156 0.2339 0.2410 REMARK 3 4 1.4768 - 1.3417 0.94 2786 144 0.2889 0.3066 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) : 32.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.56 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 105:118 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.447 -10.074 18.166 REMARK 3 T TENSOR REMARK 3 T11: 0.3593 T22: 0.2181 REMARK 3 T33: 0.1789 T12: 0.0801 REMARK 3 T13: -0.0393 T23: -0.0356 REMARK 3 L TENSOR REMARK 3 L11: 2.5711 L22: 1.8140 REMARK 3 L33: 2.8569 L12: 0.9210 REMARK 3 L13: 0.6763 L23: -1.7485 REMARK 3 S TENSOR REMARK 3 S11: -0.1663 S12: -0.4496 S13: 0.4044 REMARK 3 S21: 0.8761 S22: 0.2290 S23: -0.1586 REMARK 3 S31: -0.3194 S32: -0.2622 S33: -0.0065 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 119:143 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.505 -12.198 16.445 REMARK 3 T TENSOR REMARK 3 T11: 0.2741 T22: 0.2014 REMARK 3 T33: 0.2002 T12: 0.0446 REMARK 3 T13: -0.0084 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 2.1401 L22: 2.7990 REMARK 3 L33: 2.7772 L12: -0.9044 REMARK 3 L13: 1.5144 L23: -0.9494 REMARK 3 S TENSOR REMARK 3 S11: -0.1983 S12: -0.1251 S13: -0.1444 REMARK 3 S21: 0.1403 S22: 0.2312 S23: 0.1181 REMARK 3 S31: -0.2212 S32: -0.3809 S33: -0.0518 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 144:148 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.651 -9.127 9.298 REMARK 3 T TENSOR REMARK 3 T11: 0.5179 T22: 0.5721 REMARK 3 T33: 0.6680 T12: -0.0178 REMARK 3 T13: 0.0684 T23: 0.0272 REMARK 3 L TENSOR REMARK 3 L11: 4.1821 L22: 1.0085 REMARK 3 L33: 1.4939 L12: 1.2875 REMARK 3 L13: 2.3862 L23: 0.9936 REMARK 3 S TENSOR REMARK 3 S11: 0.1470 S12: 0.7045 S13: -0.0749 REMARK 3 S21: -0.4633 S22: -0.3049 S23: -0.2778 REMARK 3 S31: -0.6869 S32: 0.0061 S33: 0.0373 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 82:104 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.064 -16.846 17.174 REMARK 3 T TENSOR REMARK 3 T11: 0.1918 T22: 0.1954 REMARK 3 T33: 0.1763 T12: 0.0345 REMARK 3 T13: -0.0193 T23: 0.0004 REMARK 3 L TENSOR REMARK 3 L11: 2.4221 L22: 4.9792 REMARK 3 L33: 3.4340 L12: -0.3691 REMARK 3 L13: 0.8728 L23: -1.4206 REMARK 3 S TENSOR REMARK 3 S11: -0.1140 S12: -0.2153 S13: -0.0758 REMARK 3 S21: 0.1000 S22: 0.2723 S23: 0.2708 REMARK 3 S31: -0.0344 S32: -0.3465 S33: -0.1358 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 6IPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12432 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.343 REMARK 200 RESOLUTION RANGE LOW (A) : 41.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07325 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2300 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) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.37400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3H0H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 18.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRIC ACID PH 3.5 AND 25%(W/V) REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 16.32000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.16000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.48000 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 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 ASN A 72 REMARK 465 PHE A 73 REMARK 465 VAL A 74 REMARK 465 LEU A 75 REMARK 465 GLU A 76 REMARK 465 GLY A 77 REMARK 465 ASP A 78 REMARK 465 ILE A 79 REMARK 465 HIS A 80 REMARK 465 MET A 81 REMARK 465 HIS A 149 REMARK 465 HIS A 150 REMARK 465 HIS A 151 REMARK 465 HIS A 152 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 218 O HOH A 230 2.12 REMARK 500 N THR A 82 O HOH A 201 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H0H RELATED DB: PDB REMARK 900 CONTAINS THE SAME DOMAIN, BUT WITH DIFFERENT FLANKING REGIONS AND REMARK 900 WITHOUT HEXA-HISTIDINE TAG REMARK 900 RELATED ID: 3H0I RELATED DB: PDB REMARK 900 CONTAINS THE SAME DOMAIN, BUT WITH DIFFERENT FLANKING REGIONS AND REMARK 900 WITHOUT HEXA-HISTIDINE TAG DBREF 6IPY A 82 144 UNP P06241 FYN_HUMAN 82 144 SEQADV 6IPY ASN A 72 UNP P06241 EXPRESSION TAG SEQADV 6IPY PHE A 73 UNP P06241 EXPRESSION TAG SEQADV 6IPY VAL A 74 UNP P06241 EXPRESSION TAG SEQADV 6IPY LEU A 75 UNP P06241 EXPRESSION TAG SEQADV 6IPY GLU A 76 UNP P06241 EXPRESSION TAG SEQADV 6IPY GLY A 77 UNP P06241 EXPRESSION TAG SEQADV 6IPY ASP A 78 UNP P06241 EXPRESSION TAG SEQADV 6IPY ILE A 79 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 80 UNP P06241 EXPRESSION TAG SEQADV 6IPY MET A 81 UNP P06241 EXPRESSION TAG SEQADV 6IPY ILE A 96 UNP P06241 ARG 96 ENGINEERED MUTATION SEQADV 6IPY LEU A 145 UNP P06241 EXPRESSION TAG SEQADV 6IPY GLU A 146 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 147 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 148 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 149 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 150 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 151 UNP P06241 EXPRESSION TAG SEQADV 6IPY HIS A 152 UNP P06241 EXPRESSION TAG SEQRES 1 A 81 ASN PHE VAL LEU GLU GLY ASP ILE HIS MET THR GLY VAL SEQRES 2 A 81 THR LEU PHE VAL ALA LEU TYR ASP TYR GLU ALA ILE THR SEQRES 3 A 81 GLU ASP ASP LEU SER PHE HIS LYS GLY GLU LYS PHE GLN SEQRES 4 A 81 ILE LEU ASN SER SER GLU GLY ASP TRP TRP GLU ALA ARG SEQRES 5 A 81 SER LEU THR THR GLY GLU THR GLY TYR ILE PRO SER ASN SEQRES 6 A 81 TYR VAL ALA PRO VAL ASP SER ILE LEU GLU HIS HIS HIS SEQRES 7 A 81 HIS HIS HIS FORMUL 2 HOH *31(H2 O) HELIX 1 AA1 ASP A 142 ILE A 144 5 3 SHEET 1 AA1 5 THR A 130 PRO A 134 0 SHEET 2 AA1 5 TRP A 119 SER A 124 -1 N ALA A 122 O GLY A 131 SHEET 3 AA1 5 LYS A 108 ASN A 113 -1 N GLN A 110 O ARG A 123 SHEET 4 AA1 5 PHE A 87 ALA A 89 -1 N PHE A 87 O PHE A 109 SHEET 5 AA1 5 VAL A 138 PRO A 140 -1 O ALA A 139 N VAL A 88 CRYST1 41.520 41.520 32.640 90.00 90.00 90.00 P 41 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 0.024085 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024085 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030637 0.00000