HEADER HYDROLASE 06-JUL-16 5KQM TITLE CO-CRYSTAL STRUCTURE OF LMW-PTP IN COMPLEX WITH MES 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 LMW-PTP, INHIBITOR, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,Z.-Y.ZHANG,Z.-H.YU REVDAT 2 04-OCT-23 5KQM 1 JRNL REMARK REVDAT 1 12-OCT-16 5KQM 0 JRNL AUTH R.HE,J.WANG,Z.H.YU,R.Y.ZHANG,S.LIU,L.WU,Z.Y.ZHANG JRNL TITL INHIBITION OF LOW MOLECULAR WEIGHT PROTEIN TYROSINE JRNL TITL 2 PHOSPHATASE BY AN INDUCED-FIT MECHANISM. JRNL REF J.MED.CHEM. 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27676368 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00993 REMARK 2 REMARK 2 RESOLUTION. 1.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14231 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 715 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 27.4655 - 3.2610 0.99 2848 152 0.1681 0.1971 REMARK 3 2 3.2610 - 2.5890 1.00 2717 128 0.1936 0.2421 REMARK 3 3 2.5890 - 2.2619 1.00 2697 142 0.1993 0.2750 REMARK 3 4 2.2619 - 2.0552 1.00 2687 144 0.2016 0.2622 REMARK 3 5 2.0552 - 1.9100 0.97 2567 149 0.2231 0.2580 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 35.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.020 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) : 0.29870 REMARK 3 B22 (A**2) : 5.43780 REMARK 3 B33 (A**2) : -5.73650 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 1260 REMARK 3 ANGLE : 1.989 1700 REMARK 3 CHIRALITY : 0.076 182 REMARK 3 PLANARITY : 0.004 222 REMARK 3 DIHEDRAL : 16.006 483 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 5KQM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-11 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 : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 5PNT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEGME 5000, 0.2 M AMMONIUM REMARK 280 SULFATE, 100 MM MES, PH=6.5, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 16.84500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.59550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.41300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.59550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.84500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.41300 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 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 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 -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 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 OD1 ASP A 98 NH1 ARG A 101 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 HIS A 157 CA - C - O ANGL. DEV. = 38.9 DEGREES 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 MES A 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KQG RELATED DB: PDB REMARK 900 RELATED ID: 5KQL RELATED DB: PDB REMARK 900 RELATED ID: 5KQP RELATED DB: PDB DBREF 5KQM A 0 157 UNP P24666 PPAC_HUMAN 1 158 SEQADV 5KQM MET A -20 UNP P24666 INITIATING METHIONINE SEQADV 5KQM GLY A -19 UNP P24666 EXPRESSION TAG SEQADV 5KQM SER A -18 UNP P24666 EXPRESSION TAG SEQADV 5KQM SER A -17 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -16 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -15 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -14 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -13 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -12 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -11 UNP P24666 EXPRESSION TAG SEQADV 5KQM SER A -10 UNP P24666 EXPRESSION TAG SEQADV 5KQM SER A -9 UNP P24666 EXPRESSION TAG SEQADV 5KQM GLY A -8 UNP P24666 EXPRESSION TAG SEQADV 5KQM LEU A -7 UNP P24666 EXPRESSION TAG SEQADV 5KQM VAL A -6 UNP P24666 EXPRESSION TAG SEQADV 5KQM PRO A -5 UNP P24666 EXPRESSION TAG SEQADV 5KQM ARG A -4 UNP P24666 EXPRESSION TAG SEQADV 5KQM GLY A -3 UNP P24666 EXPRESSION TAG SEQADV 5KQM SER A -2 UNP P24666 EXPRESSION TAG SEQADV 5KQM HIS A -1 UNP P24666 EXPRESSION TAG SEQRES 1 A 178 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 178 LEU VAL PRO ARG GLY SER HIS MET ALA GLU GLN ALA THR SEQRES 3 A 178 LYS SER VAL LEU PHE VAL CYS LEU GLY ASN ILE CYS ARG SEQRES 4 A 178 SER PRO ILE ALA GLU ALA VAL PHE ARG LYS LEU VAL THR SEQRES 5 A 178 ASP GLN ASN ILE SER GLU ASN TRP ARG VAL ASP SER ALA SEQRES 6 A 178 ALA THR SER GLY TYR GLU ILE GLY ASN PRO PRO ASP TYR SEQRES 7 A 178 ARG GLY GLN SER CYS MET LYS ARG HIS GLY ILE PRO MET SEQRES 8 A 178 SER HIS VAL ALA ARG GLN ILE THR LYS GLU ASP PHE ALA SEQRES 9 A 178 THR PHE ASP TYR ILE LEU CYS MET ASP GLU SER ASN LEU SEQRES 10 A 178 ARG ASP LEU ASN ARG LYS SER ASN GLN VAL LYS THR CYS SEQRES 11 A 178 LYS ALA LYS ILE GLU LEU LEU GLY SER TYR ASP PRO GLN SEQRES 12 A 178 LYS GLN LEU ILE ILE GLU ASP PRO TYR TYR GLY ASN ASP SEQRES 13 A 178 SER ASP PHE GLU THR VAL TYR GLN GLN CYS VAL ARG CYS SEQRES 14 A 178 CYS ARG ALA PHE LEU GLU LYS ALA HIS HET MES A 200 12 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 2 MES C6 H13 N O4 S FORMUL 3 HOH *121(H2 O) HELIX 1 AA1 ARG A 18 GLN A 33 1 16 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 LYS A 6 O ARG 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 LYS A 112 N ILE A 88 SITE 1 AC1 12 CYS A 12 LEU A 13 GLY A 14 ASN A 15 SITE 2 AC1 12 ILE A 16 CYS A 17 ARG A 18 GLU A 50 SITE 3 AC1 12 ARG A 97 ASP A 129 TYR A 131 HOH A 335 CRYST1 33.690 54.826 95.191 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 0.029682 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010505 0.00000