HEADER HYDROLASE 27-JUL-22 8DU7 TITLE ROOM-TEMPERATURE SERIAL SYNCHROTRON CRYSTALLOGRAPHY (SSX) STRUCTURE OF TITLE 2 APO PTP1B COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 5 EC: 3.1.3.48; 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: PTPN1, PTP1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTEIN TYROSINE PHOSPHATASE, PTP, PROTEIN TYROSINE PHOSPHATASE 1B, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.EBRAHIM,S.SHARMA,D.A.KEEDY REVDAT 3 25-OCT-23 8DU7 1 REMARK REVDAT 2 18-JAN-23 8DU7 1 JRNL REVDAT 1 17-AUG-22 8DU7 0 JRNL AUTH S.SHARMA,A.EBRAHIM,D.A.KEEDY JRNL TITL ROOM-TEMPERATURE SERIAL SYNCHROTRON CRYSTALLOGRAPHY OF THE JRNL TITL 2 HUMAN PHOSPHATASE PTP1B. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 79 23 2023 JRNL REFN ESSN 2053-230X JRNL PMID 36598353 JRNL DOI 10.1107/S2053230X22011645 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.EBRAHIM,S.SHARMA,D.A.KEEDY REMARK 1 TITL ROOM-TEMPERATURE SERIAL SYNCHROTRON CRYSTALLOGRAPHY OF APO REMARK 1 TITL 2 PTP1B REMARK 1 REF BIORXIV 2022 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.07.28.501725 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 18931 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 942 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 44.6800 - 4.5900 0.99 2770 146 0.1730 0.2042 REMARK 3 2 4.5900 - 3.6400 1.00 2648 139 0.1458 0.1857 REMARK 3 3 3.6400 - 3.1800 1.00 2668 140 0.1903 0.2199 REMARK 3 4 3.1800 - 2.8900 0.99 2607 138 0.2277 0.2862 REMARK 3 5 2.8900 - 2.6800 0.99 2604 138 0.2705 0.3598 REMARK 3 6 2.6800 - 2.5300 0.94 2448 127 0.2900 0.3322 REMARK 3 7 2.5300 - 2.4000 0.86 2244 114 0.3210 0.3832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.372 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.228 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.87 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 : 0.013 2454 REMARK 3 ANGLE : 1.326 3308 REMARK 3 CHIRALITY : 0.061 350 REMARK 3 PLANARITY : 0.021 427 REMARK 3 DIHEDRAL : 7.894 326 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 8DU7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : 7B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9686 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DUAL BOUNCE W/B4C MULTILAYER REMARK 200 MONOCHROMATOR. COMPOUND REMARK 200 REFRACTIVE LENS FOR MICROBEAM REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JAN 10, 2022 REMARK 200 BUILT=20220220 REMARK 200 DATA SCALING SOFTWARE : XSCALE VERSION JAN 10, 2022 REMARK 200 BUILT=20220220 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19515 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 44.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.45 REMARK 200 R MERGE (I) : 0.66100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 11.06 REMARK 200 R MERGE FOR SHELL (I) : 4.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 1T49 REMARK 200 REMARK 200 REMARK: CUBOID REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MGCL2, 0.1 M HEPES PH 7.0, 12 REMARK 280 -14.5% PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.25333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 70.50667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 70.50667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.25333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 OH TYR A 152 HD22 ASN A 193 1.53 REMARK 500 HE ARG A 105 O HOH A 405 1.55 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 SER A 13 1.33 -65.48 REMARK 500 SER A 15 42.93 -85.06 REMARK 500 CYS A 121 138.84 -174.93 REMARK 500 THR A 165 -9.01 -144.40 REMARK 500 PRO A 180 140.54 -39.21 REMARK 500 CYS A 215 -134.06 -134.99 REMARK 500 ILE A 219 -32.29 -139.38 REMARK 500 LYS A 239 56.67 34.22 REMARK 500 PRO A 241 28.53 -79.83 REMARK 500 SER A 242 2.35 -151.87 REMARK 500 SER A 242 12.89 -67.91 REMARK 500 ILE A 261 105.20 71.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 24 0.10 SIDE CHAIN REMARK 500 ARG A 79 0.15 SIDE CHAIN REMARK 500 ARG A 268 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8DU7 A 1 284 UNP P18031 PTN1_HUMAN 1 284 SEQADV 8DU7 SER A 32 UNP P18031 CYS 32 ENGINEERED MUTATION SEQADV 8DU7 VAL A 92 UNP P18031 CYS 92 ENGINEERED MUTATION SEQRES 1 A 284 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER SEQRES 2 A 284 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU SEQRES 3 A 284 ALA SER ASP PHE PRO SER ARG VAL ALA LYS LEU PRO LYS SEQRES 4 A 284 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE SEQRES 5 A 284 ASP HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP SEQRES 6 A 284 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN SEQRES 7 A 284 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR SEQRES 8 A 284 VAL GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER SEQRES 9 A 284 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SEQRES 10 A 284 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU SEQRES 11 A 284 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR SEQRES 12 A 284 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG SEQRES 13 A 284 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG SEQRES 14 A 284 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP PHE SEQRES 15 A 284 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU SEQRES 16 A 284 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS SEQRES 17 A 284 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG SEQRES 18 A 284 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU SEQRES 19 A 284 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS SEQRES 20 A 284 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU SEQRES 21 A 284 ILE GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA SEQRES 22 A 284 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP HET TRS A 301 20 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 HOH *63(H2 O) HELIX 1 AA1 MET A 1 SER A 13 1 13 HELIX 2 AA2 SER A 15 ALA A 27 1 13 HELIX 3 AA3 SER A 32 LEU A 37 1 6 HELIX 4 AA4 PRO A 38 ASN A 44 5 7 HELIX 5 AA5 THR A 91 LYS A 103 1 13 HELIX 6 AA6 PRO A 188 SER A 201 1 14 HELIX 7 AA7 GLY A 220 ARG A 238 1 19 HELIX 8 AA8 ASP A 245 ARG A 254 1 10 HELIX 9 AA9 THR A 263 PHE A 280 1 18 SHEET 1 AA1 9 ARG A 56 LYS A 58 0 SHEET 2 AA1 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57 SHEET 3 AA1 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72 SHEET 4 AA1 9 VAL A 211 HIS A 214 1 O VAL A 213 N ILE A 82 SHEET 5 AA1 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212 SHEET 6 AA1 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N LEU A 160 O ARG A 169 SHEET 8 AA1 9 LEU A 140 ILE A 149 -1 N LYS A 141 O GLU A 161 SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140 SHEET 1 AA2 2 MET A 114 GLU A 115 0 SHEET 2 AA2 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115 CRYST1 89.350 89.350 105.760 90.00 90.00 120.00 P 31 2 1 6 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 0.011192 0.006462 0.000000 0.00000 SCALE2 0.000000 0.012923 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009455 0.00000