HEADER STRUCTURAL PROTEIN 07-JUN-24 9C66 TITLE STRUCTURE OF THE MENA EVH1 DOMAIN BOUND TO THE POLYPROLINE SEGMENT OF TITLE 2 PTP1B COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ENABLED HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POLY-PROLINE SEGMENT OF PTP1B; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ENAH, MENA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX4T-1; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS MENA, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.LACOMB,E.FEDOROV,J.B.BONANNO,S.C.ALMO,A.GHOSH REVDAT 2 11-SEP-24 9C66 1 JRNL REVDAT 1 28-AUG-24 9C66 0 JRNL AUTH L.LACOMB,A.GHOSH,J.B.BONANNO,D.J.NILSON,A.J.POPPEL,L.DADA, JRNL AUTH 2 S.M.CAHILL,J.P.MAIANTI,S.KITAMURA,D.COWBURN,S.C.ALMO JRNL TITL INSIGHTS INTO THE INTERACTION LANDSCAPE OF THE EVH1 DOMAIN JRNL TITL 2 OF MENA. JRNL REF BIOCHEMISTRY V. 63 2183 2024 JRNL REFN ISSN 0006-2960 JRNL PMID 39138154 JRNL DOI 10.1021/ACS.BIOCHEM.4C00331 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21RC1_5156) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 21323 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1060 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 19.8300 - 2.8000 1.00 2716 115 0.1835 0.1716 REMARK 3 2 2.8000 - 2.2200 1.00 2554 149 0.1813 0.1858 REMARK 3 3 2.2200 - 1.9400 1.00 2556 123 0.1735 0.2011 REMARK 3 4 1.9400 - 1.7600 0.99 2486 138 0.1790 0.1907 REMARK 3 5 1.7600 - 1.6400 1.00 2531 115 0.1904 0.2313 REMARK 3 6 1.6400 - 1.5400 1.00 2496 125 0.2009 0.2058 REMARK 3 7 1.5400 - 1.4600 0.98 2456 137 0.2162 0.2316 REMARK 3 8 1.4600 - 1.4000 1.00 2468 158 0.2521 0.2926 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) : 20.050 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 : 0.015 NULL REMARK 3 ANGLE : 1.472 NULL REMARK 3 CHIRALITY : 0.098 146 REMARK 3 PLANARITY : 0.013 177 REMARK 3 DIHEDRAL : 16.943 353 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 9C66 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000284874. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97932 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 : 21372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 12.00 REMARK 200 R MERGE FOR SHELL (I) : 0.57700 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 (%): 34.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE AND 0.1 M BIS REMARK 280 -TRIS, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 19.82700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.05250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.53600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.05250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.82700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.53600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU B 304 REMARK 465 HIS B 305 REMARK 465 ARG B 311 REMARK 465 PRO B 312 REMARK 465 PRO B 313 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 21 CD CE NZ REMARK 470 LYS A 22 CD CE NZ REMARK 470 ARG A 81 CD NE CZ NH1 NH2 REMARK 470 ARG A 84 CD NE CZ NH1 NH2 REMARK 470 LYS A 94 CE NZ REMARK 470 GLU A 95 CD OE1 OE2 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 ASN A 61 88.81 -155.89 REMARK 500 ALA A 83 30.01 79.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 9C66 A 1 113 UNP Q8N8S7 ENAH_HUMAN 1 113 DBREF 9C66 B 304 313 UNP P18031 PTN1_HUMAN 304 313 SEQADV 9C66 SER A 0 UNP Q8N8S7 EXPRESSION TAG SEQRES 1 A 114 SER MET SER GLU GLN SER ILE CSO GLN ALA ARG ALA ALA SEQRES 2 A 114 VAL MET VAL TYR ASP ASP ALA ASN LYS LYS TRP VAL PRO SEQRES 3 A 114 ALA GLY GLY SER THR GLY PHE SER ARG VAL HIS ILE TYR SEQRES 4 A 114 HIS HIS THR GLY ASN ASN THR PHE ARG VAL VAL GLY ARG SEQRES 5 A 114 LYS ILE GLN ASP HIS GLN VAL VAL ILE ASN CME ALA ILE SEQRES 6 A 114 PRO LYS GLY LEU LYS TYR ASN GLN ALA THR GLN THR PHE SEQRES 7 A 114 HIS GLN TRP ARG ASP ALA ARG GLN VAL TYR GLY LEU ASN SEQRES 8 A 114 PHE GLY SER LYS GLU ASP ALA ASN VAL PHE ALA SER ALA SEQRES 9 A 114 MET MET HIS ALA LEU GLU VAL LEU ASN SER SEQRES 1 B 10 GLU HIS ILE PRO PRO PRO PRO ARG PRO PRO MODRES 9C66 CSO A 7 CYS MODIFIED RESIDUE MODRES 9C66 CME A 62 CYS MODIFIED RESIDUE HET CSO A 7 12 HET CME A 62 18 HET EDO A 201 10 HET EDO A 202 10 HET SO4 A 203 5 HETNAM CSO S-HYDROXYCYSTEINE HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CSO C3 H7 N O3 S FORMUL 1 CME C5 H11 N O3 S2 FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *63(H2 O) HELIX 1 AA1 SER A 2 CSO A 7 1 6 HELIX 2 AA2 GLY A 27 SER A 29 5 3 HELIX 3 AA3 THR A 41 ASN A 44 5 4 HELIX 4 AA4 SER A 93 ASN A 112 1 20 SHEET 1 AA1 5 LYS A 22 PRO A 25 0 SHEET 2 AA1 5 GLN A 8 ASP A 17 -1 N ASP A 17 O LYS A 22 SHEET 3 AA1 5 PHE A 32 HIS A 40 -1 O SER A 33 N ALA A 11 SHEET 4 AA1 5 THR A 45 LYS A 52 -1 O VAL A 49 N HIS A 36 SHEET 5 AA1 5 VAL A 58 ALA A 63 -1 O ILE A 60 N GLY A 50 SHEET 1 AA2 5 LYS A 22 PRO A 25 0 SHEET 2 AA2 5 GLN A 8 ASP A 17 -1 N ASP A 17 O LYS A 22 SHEET 3 AA2 5 VAL A 86 PHE A 91 -1 O GLY A 88 N MET A 14 SHEET 4 AA2 5 PHE A 77 ARG A 81 -1 N HIS A 78 O LEU A 89 SHEET 5 AA2 5 ASN A 71 GLN A 72 -1 N ASN A 71 O GLN A 79 LINK C ILE A 6 N CSO A 7 1555 1555 1.33 LINK C CSO A 7 N GLN A 8 1555 1555 1.32 LINK C ASN A 61 N CME A 62 1555 1555 1.31 LINK C CME A 62 N ALA A 63 1555 1555 1.32 CRYST1 39.654 49.072 54.105 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 0.025218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020378 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018483 0.00000