HEADER HYDROLASE 17-FEB-20 6Y2W TITLE CRYSTAL STRUCTURE OF THE SINGLE MUTANT I16K OF LOW MOLECULAR WEIGHT TITLE 2 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 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 6Y2W 1 REMARK REVDAT 1 22-JUL-20 6Y2W 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. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 13525 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 679 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 33.6400 - 3.0200 0.94 2659 130 0.1503 0.1947 REMARK 3 2 3.0200 - 2.4000 0.99 2704 140 0.1656 0.1814 REMARK 3 3 2.4000 - 2.1000 0.99 2684 139 0.1632 0.1923 REMARK 3 4 2.1000 - 1.9100 0.85 2330 112 0.1833 0.2020 REMARK 3 5 1.9100 - 1.7700 0.93 2469 158 0.2517 0.2725 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) : 0.233 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.93 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 1308 REMARK 3 ANGLE : 1.179 1774 REMARK 3 CHIRALITY : 0.060 191 REMARK 3 PLANARITY : 0.008 238 REMARK 3 DIHEDRAL : 6.379 180 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): -17.8958 -0.9246 17.2707 REMARK 3 T TENSOR REMARK 3 T11: 0.2241 T22: 0.1938 REMARK 3 T33: 0.1929 T12: -0.0250 REMARK 3 T13: 0.0096 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.7482 L22: 1.3907 REMARK 3 L33: 1.0645 L12: 0.3556 REMARK 3 L13: 0.3892 L23: -0.3351 REMARK 3 S TENSOR REMARK 3 S11: -0.1666 S12: 0.0200 S13: 0.0255 REMARK 3 S21: -0.1929 S22: 0.1017 S23: -0.0617 REMARK 3 S31: 0.0340 S32: -0.0650 S33: -0.0012 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 6Y2W 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_1292106786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 33.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.160 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 (%): 40.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM ACETATE TRIHYDRATE, 0.1M REMARK 280 BIS-TRIS, 25% PEG3350, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 28.57600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.57600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.88000 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 CH3 ACT A 201 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 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 1.67 REMARK 500 O HOH A 407 O HOH A 435 1.87 REMARK 500 O HOH A 404 O HOH A 435 2.04 REMARK 500 O HOH A 396 O HOH A 413 2.06 REMARK 500 O HOH A 319 O HOH A 415 2.12 REMARK 500 O HOH A 334 O HOH A 375 2.15 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 CYS A 17 -74.88 -113.16 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 ACT A 201 DBREF 6Y2W A 1 157 UNP P24666 PPAC_HUMAN 2 158 SEQADV 6Y2W LYS A 16 UNP P24666 ILE 17 ENGINEERED MUTATION SEQRES 1 A 157 ALA GLU GLN ALA THR LYS SER VAL LEU PHE VAL CYS LEU SEQRES 2 A 157 GLY ASN LYS CYS ARG SER PRO ILE ALA GLU ALA VAL PHE SEQRES 3 A 157 ARG LYS LEU VAL THR ASP GLN ASN ILE SER GLU ASN TRP SEQRES 4 A 157 VAL ILE ASP SER GLY ALA VAL SER ASP TRP ASN VAL GLY SEQRES 5 A 157 ARG SER PRO ASP PRO ARG ALA VAL SER CYS LEU ARG ASN SEQRES 6 A 157 HIS GLY ILE HIS THR ALA HIS LYS ALA ARG GLN ILE THR SEQRES 7 A 157 LYS GLU ASP PHE ALA THR PHE ASP TYR ILE LEU CYS MET SEQRES 8 A 157 ASP GLU SER ASN LEU ARG ASP LEU ASN ARG LYS SER ASN SEQRES 9 A 157 GLN VAL LYS THR CYS LYS ALA LYS ILE GLU LEU LEU GLY SEQRES 10 A 157 SER TYR ASP PRO GLN LYS GLN LEU ILE ILE GLU ASP PRO SEQRES 11 A 157 TYR TYR GLY ASN ASP SER ASP PHE GLU THR VAL TYR GLN SEQRES 12 A 157 GLN CYS VAL ARG CYS CYS ARG ALA PHE LEU GLU LYS ALA SEQRES 13 A 157 HIS HET ACT A 201 7 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *138(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 ASN A 104 1 13 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 PHE A 10 O GLY A 44 SHEET 3 AA1 4 TYR A 87 CYS A 90 1 O LEU A 89 N LEU A 9 SHEET 4 AA1 4 LYS A 112 LEU A 115 1 O LYS A 112 N ILE A 88 SITE 1 AC1 4 PRO A 57 ARG A 58 SER A 61 ASP A 135 CRYST1 57.152 41.760 62.150 90.00 96.57 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 0.017497 0.000000 0.002016 0.00000 SCALE2 0.000000 0.023946 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016197 0.00000