HEADER HYDROLASE 17-FEB-20 6Y2V TITLE CRYSTAL STRUCTURE OF THE DOUBLE MUTANT L13R I16K OF LOW MOLECULAR TITLE 2 WEIGHT PROTEIN TYROSINE PHOSPHATASE (LMW-PTP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LMW-PTPASE,ADIPOCYTE ACID PHOSPHATASE,LOW MOLECULAR WEIGHT COMPND 5 CYTOSOLIC ACID PHOSPHATASE,RED CELL ACID PHOSPHATASE 1; COMPND 6 EC: 3.1.3.48,3.1.3.2; 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: ACP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ENGINEERED, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.LEVY REVDAT 2 24-JAN-24 6Y2V 1 REMARK REVDAT 1 22-JUL-20 6Y2V 0 JRNL AUTH E.EGBE,C.W.LEVY,L.TABERNERO JRNL TITL COMPUTATIONAL AND STRUCTURE-GUIDED DESIGN OF JRNL TITL 2 PHOSPHOINOSITIDE SUBSTRATE SPECIFICITY INTO THE TYROSINE JRNL TITL 3 SPECIFIC LMW-PTP ENZYME. JRNL REF PLOS ONE V. 15 35133 2020 JRNL REFN ESSN 1932-6203 JRNL PMID 32584877 JRNL DOI 10.1371/JOURNAL.PONE.0235133 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 8999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.330 REMARK 3 FREE R VALUE TEST SET COUNT : 480 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 33.3600 - 2.8800 0.99 2874 161 0.1636 0.2206 REMARK 3 2 2.8800 - 2.2800 0.99 2800 167 0.2034 0.2305 REMARK 3 3 2.2800 - 2.0000 1.00 2845 152 0.2181 0.2700 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) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.879 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.64 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 : 0.002 1274 REMARK 3 ANGLE : 0.472 1717 REMARK 3 CHIRALITY : 0.042 185 REMARK 3 PLANARITY : 0.003 224 REMARK 3 DIHEDRAL : 22.000 176 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -14.7011 0.8163 14.4903 REMARK 3 T TENSOR REMARK 3 T11: 0.1437 T22: 0.0926 REMARK 3 T33: 0.1490 T12: -0.0216 REMARK 3 T13: -0.0064 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 2.4080 L22: 1.5209 REMARK 3 L33: 2.4634 L12: 0.1106 REMARK 3 L13: 0.0371 L23: -0.5203 REMARK 3 S TENSOR REMARK 3 S11: -0.0370 S12: 0.0078 S13: 0.1223 REMARK 3 S21: -0.1546 S22: 0.0495 S23: -0.0084 REMARK 3 S31: 0.0149 S32: -0.1631 S33: -0.0027 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 6Y2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1292106783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-17 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 : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9025 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 33.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.020 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: 1XWW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 25% PEG3350, PH 5.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.31250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.64350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.31250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.64350 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 361 LIES ON A SPECIAL POSITION. 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 MET A 0 REMARK 465 ALA A 1 REMARK 465 GLU A 2 REMARK 465 GLN A 3 REMARK 465 ALA A 4 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 OD2 ASP A 135 O HOH A 301 2.05 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 ILE A 35 17.20 -141.42 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 PGE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 202 DBREF 6Y2V A 0 157 UNP P24666 PPAC_HUMAN 1 158 SEQADV 6Y2V ARG A 13 UNP P24666 LEU 14 ENGINEERED MUTATION SEQADV 6Y2V LYS A 16 UNP P24666 ILE 17 ENGINEERED MUTATION SEQRES 1 A 158 MET ALA GLU GLN ALA THR LYS SER VAL LEU PHE VAL CYS SEQRES 2 A 158 ARG GLY ASN LYS CYS ARG SER PRO ILE ALA GLU ALA VAL SEQRES 3 A 158 PHE ARG LYS LEU VAL THR ASP GLN ASN ILE SER GLU ASN SEQRES 4 A 158 TRP VAL ILE ASP SER GLY ALA VAL SER ASP TRP ASN VAL SEQRES 5 A 158 GLY ARG SER PRO ASP PRO ARG ALA VAL SER CYS LEU ARG SEQRES 6 A 158 ASN HIS GLY ILE HIS THR ALA HIS LYS ALA ARG GLN ILE SEQRES 7 A 158 THR LYS GLU ASP PHE ALA THR PHE ASP TYR ILE LEU CYS SEQRES 8 A 158 MET ASP GLU SER ASN LEU ARG ASP LEU ASN ARG LYS SER SEQRES 9 A 158 ASN GLN VAL LYS THR CYS LYS ALA LYS ILE GLU LEU LEU SEQRES 10 A 158 GLY SER TYR ASP PRO GLN LYS GLN LEU ILE ILE GLU ASP SEQRES 11 A 158 PRO TYR TYR GLY ASN ASP SER ASP PHE GLU THR VAL TYR SEQRES 12 A 158 GLN GLN CYS VAL ARG CYS CYS ARG ALA PHE LEU GLU LYS SEQRES 13 A 158 ALA HIS HET PGE A 201 24 HET PO4 A 202 5 HETNAM PGE TRIETHYLENE GLYCOL HETNAM PO4 PHOSPHATE ION FORMUL 2 PGE C6 H14 O4 FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *85(H2 O) HELIX 1 AA1 CYS A 17 GLN A 33 1 17 HELIX 2 AA2 ILE A 35 GLU A 37 5 3 HELIX 3 AA3 ASP A 56 HIS A 66 1 11 HELIX 4 AA4 THR A 78 PHE A 85 1 8 HELIX 5 AA5 ASP A 92 GLN A 105 1 14 HELIX 6 AA6 GLY A 117 ASP A 120 5 4 HELIX 7 AA7 ASN A 134 LYS A 155 1 22 SHEET 1 AA1 4 TRP A 39 ALA A 45 0 SHEET 2 AA1 4 LYS A 6 CYS A 12 1 N LYS A 6 O VAL A 40 SHEET 3 AA1 4 TYR A 87 CYS A 90 1 O TYR A 87 N LEU A 9 SHEET 4 AA1 4 LYS A 112 LEU A 115 1 O GLU A 114 N ILE A 88 SITE 1 AC1 5 GLU A 80 THR A 84 ASP A 98 LYS A 102 SITE 2 AC1 5 GLN A 105 SITE 1 AC2 8 CYS A 12 ARG A 13 GLY A 14 ASN A 15 SITE 2 AC2 8 LYS A 16 CYS A 17 ARG A 18 ASP A 129 CRYST1 56.625 41.287 56.898 90.00 91.81 90.00 C 1 2 1 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 0.017660 0.000000 0.000558 0.00000 SCALE2 0.000000 0.024221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017584 0.00000