HEADER HYDROLASE 15-APR-19 6OL4 TITLE PROTEIN TYROSINE PHOSPHATASE 1B (1-301), F182A MUTANT, APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2-297; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 6 EC: 3.1.3.48; COMPND 7 ENGINEERED: YES; COMPND 8 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS PTP1B, PTP, MULTICONFORMER, SIGNALING PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.S.CUI,J.M.LIPCHOCK,J.P.LORIA REVDAT 3 15-NOV-23 6OL4 1 REMARK REVDAT 2 11-OCT-23 6OL4 1 REMARK REVDAT 1 25-MAR-20 6OL4 0 JRNL AUTH D.S.CUI,J.M.LIPCHOCK,D.BROOKNER,J.P.LORIA JRNL TITL UNCOVERING THE MOLECULAR INTERACTIONS IN THE CATALYTIC LOOP JRNL TITL 2 THAT MODULATE THE CONFORMATIONAL DYNAMICS IN PROTEIN JRNL TITL 3 TYROSINE PHOSPHATASE 1B. JRNL REF J.AM.CHEM.SOC. V. 141 12634 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31339043 JRNL DOI 10.1021/JACS.9B04470 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 24822 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 31.4900 - 4.4600 0.99 2833 0 0.1673 0.1917 REMARK 3 2 4.4600 - 3.5400 0.99 2716 0 0.1621 0.1976 REMARK 3 3 3.5400 - 3.1000 0.97 2654 0 0.2066 0.2635 REMARK 3 4 3.1000 - 2.8200 0.90 2436 0 0.2877 0.3529 REMARK 3 5 2.8200 - 2.6100 0.91 2452 0 0.3068 0.3455 REMARK 3 6 2.6100 - 2.4600 0.95 2545 0 0.3148 0.4302 REMARK 3 7 2.4600 - 2.3300 0.97 2658 0 0.2974 0.3197 REMARK 3 8 2.3300 - 2.2300 0.98 2603 0 0.3099 0.3873 REMARK 3 9 2.2300 - 2.1500 0.99 2664 0 0.2927 0.3599 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.93 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 : 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 : 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 6OL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000240816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25757 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 35.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.10770 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.72560 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: 3QKQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.2 M MAGNESIUM ACETATE REMARK 280 AND 15-20% POLYETHYLENE GLYCOL 8000, PH 7, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 34.58033 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 69.16067 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 69.16067 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 34.58033 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 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 5 CG CD CE NZ 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 ASP A 63 -73.68 -72.51 REMARK 500 CYS A 121 134.41 -177.02 REMARK 500 LYS A 131 76.29 -114.33 REMARK 500 GLN A 166 3.34 59.21 REMARK 500 ALA A 182 16.00 57.55 REMARK 500 OCS A 215 -130.65 -122.87 REMARK 500 ILE A 219 -38.36 -137.39 REMARK 500 ASP A 240 79.79 -118.37 REMARK 500 ASP A 240 78.09 -152.73 REMARK 500 ILE A 261 108.30 73.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 DBREF 6OL4 A 2 297 UNP P18031 PTN1_HUMAN 2 297 SEQADV 6OL4 ALA A 182 UNP P18031 PHE 182 ENGINEERED MUTATION SEQRES 1 A 296 GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER GLY SEQRES 2 A 296 SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU ALA SEQRES 3 A 296 SER ASP PHE PRO CYS ARG VAL ALA LYS LEU PRO LYS ASN SEQRES 4 A 296 LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE ASP SEQRES 5 A 296 HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP TYR SEQRES 6 A 296 ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN ARG SEQRES 7 A 296 SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR CYS SEQRES 8 A 296 GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER ARG SEQRES 9 A 296 GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SER SEQRES 10 A 296 LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU LYS SEQRES 11 A 296 GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR LEU SEQRES 12 A 296 ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG GLN SEQRES 13 A 296 LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG GLU SEQRES 14 A 296 ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP ALA GLY SEQRES 15 A 296 VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU PHE SEQRES 16 A 296 LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS GLY SEQRES 17 A 296 PRO VAL VAL VAL HIS OCS SER ALA GLY ILE GLY ARG SER SEQRES 18 A 296 GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU MET SEQRES 19 A 296 ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS LYS SEQRES 20 A 296 VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU ILE SEQRES 21 A 296 GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA VAL SEQRES 22 A 296 ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER VAL SEQRES 23 A 296 GLN ASP GLN TRP LYS GLU LEU SER HIS GLU MODRES 6OL4 OCS A 215 CYS MODIFIED RESIDUE HET OCS A 215 9 HET GOL A 301 6 HET GOL A 302 6 HET GOL A 303 6 HETNAM OCS CYSTEINESULFONIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 OCS C3 H7 N O5 S FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 HOH *171(H2 O) HELIX 1 AA1 GLU A 2 SER A 13 1 12 HELIX 2 AA2 SER A 15 ALA A 27 1 13 HELIX 3 AA3 CYS A 32 LEU A 37 1 6 HELIX 4 AA4 PRO A 38 ASN A 44 5 7 HELIX 5 AA5 THR A 91 GLN A 102 1 12 HELIX 6 AA6 PRO A 188 SER A 201 1 14 HELIX 7 AA7 GLY A 220 LYS A 239 1 20 HELIX 8 AA8 ASP A 240 VAL A 244 5 5 HELIX 9 AA9 ASP A 245 ARG A 254 1 10 HELIX 10 AB1 THR A 263 MET A 282 1 20 HELIX 11 AB2 SER A 286 HIS A 296 1 11 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 ILE A 145 O GLN A 157 SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N MET A 133 O LEU A 142 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 LINK C HIS A 214 N OCS A 215 1555 1555 1.33 LINK C OCS A 215 N SER A 216 1555 1555 1.33 SITE 1 AC1 4 HIS A 54 GLU A 129 GLU A 130 HOH A 477 SITE 1 AC2 6 PRO A 89 MET A 133 PHE A 135 LYS A 239 SITE 2 AC2 6 HOH A 408 HOH A 508 SITE 1 AC3 5 GLU A 26 ALA A 27 GLU A 159 GLU A 161 SITE 2 AC3 5 HOH A 502 CRYST1 88.086 88.086 103.741 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 0.011353 0.006554 0.000000 0.00000 SCALE2 0.000000 0.013109 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009639 0.00000