HEADER HYDROLASE 22-MAR-22 7XC0 TITLE CRYSTAL STRUCTURE OF HUMAN RPTPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: R-PTP-H,STOMACH CANCER-ASSOCIATED PROTEIN TYROSINE COMPND 5 PHOSPHATASE 1,SAP-1,TRANSMEMBRANE-TYPE PROTEIN-TYROSINE PHOSPHATASE COMPND 6 TYPE H; COMPND 7 EC: 3.1.3.48; COMPND 8 ENGINEERED: YES; COMPND 9 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: PTPRH, SAP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KIM,S.E.RYU REVDAT 3 29-NOV-23 7XC0 1 REMARK REVDAT 2 20-JUL-22 7XC0 1 JRNL REVDAT 1 06-JUL-22 7XC0 0 JRNL AUTH M.KIM,S.E.RYU JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN RPTPH. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 78 265 2022 JRNL REFN ESSN 2053-230X JRNL PMID 35787553 JRNL DOI 10.1107/S2053230X22006173 REMARK 2 REMARK 2 RESOLUTION. 1.56 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.150 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 38471 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1980 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 24.4500 - 3.7500 0.93 2559 143 0.1444 0.1847 REMARK 3 2 3.7500 - 2.9800 0.99 2741 154 0.1565 0.2018 REMARK 3 3 2.9800 - 2.6000 0.99 2796 140 0.1811 0.1902 REMARK 3 4 2.6000 - 2.3700 0.99 2745 153 0.1900 0.2025 REMARK 3 5 2.3700 - 2.2000 0.98 2723 149 0.1898 0.2124 REMARK 3 6 2.2000 - 2.0700 0.98 2671 157 0.2025 0.2157 REMARK 3 7 2.0700 - 1.9600 0.96 2671 147 0.2121 0.2012 REMARK 3 8 1.9600 - 1.8800 0.95 2629 145 0.1725 0.2223 REMARK 3 9 1.8800 - 1.8100 0.94 2617 133 0.1886 0.2403 REMARK 3 10 1.8100 - 1.7400 0.93 2613 135 0.2236 0.2217 REMARK 3 11 1.7400 - 1.6900 0.91 2471 134 0.2261 0.2730 REMARK 3 12 1.6900 - 1.6400 0.90 2475 141 0.2478 0.2888 REMARK 3 13 1.6400 - 1.6000 0.88 2468 124 0.2751 0.3129 REMARK 3 14 1.6000 - 1.5600 0.87 2371 125 0.2927 0.3113 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) : 0.191 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.64 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 : 0.003 2388 REMARK 3 ANGLE : 0.599 3251 REMARK 3 CHIRALITY : 0.043 344 REMARK 3 PLANARITY : 0.004 426 REMARK 3 DIHEDRAL : 5.546 313 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 7XC0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-21 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 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-2000 V715 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V715 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38471 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 24.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06940 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31670 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.890 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: 2NZ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES-NAOH PH 6.5, 13%(V/V) PEGMME REMARK 280 550, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 53.63133 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 26.81567 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 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 GLY A 796 REMARK 465 ALA A 1084 REMARK 465 GLN A 1085 REMARK 465 ALA A 1086 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 833 40.23 -90.47 REMARK 500 SER A1020 -129.27 -131.53 REMARK 500 VAL A1024 -42.80 -131.12 REMARK 500 VAL A1063 91.47 61.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XC0 A 797 1086 UNP Q9HD43 PTPRH_HUMAN 797 1086 SEQADV 7XC0 GLY A 796 UNP Q9HD43 EXPRESSION TAG SEQADV 7XC0 ALA A 818 UNP Q9HD43 CYS 818 ENGINEERED MUTATION SEQADV 7XC0 SER A 1020 UNP Q9HD43 CYS 1020 ENGINEERED MUTATION SEQRES 1 A 291 GLY PRO GLY ASP ILE PRO ALA GLU ASP PHE ALA ASP HIS SEQRES 2 A 291 VAL ARG LYS ASN GLU ARG ASP SER ASN ALA GLY PHE ALA SEQRES 3 A 291 ASP GLU TYR GLN GLN LEU SER LEU VAL GLY HIS SER GLN SEQRES 4 A 291 SER GLN MET VAL ALA SER ALA SER GLU ASN ASN ALA LYS SEQRES 5 A 291 ASN ARG TYR ARG ASN VAL LEU PRO TYR ASP TRP SER ARG SEQRES 6 A 291 VAL PRO LEU LYS PRO ILE HIS GLU GLU PRO GLY SER ASP SEQRES 7 A 291 TYR ILE ASN ALA SER PHE MET PRO GLY LEU TRP SER PRO SEQRES 8 A 291 GLN GLU PHE ILE ALA THR GLN GLY PRO LEU PRO GLN THR SEQRES 9 A 291 VAL GLY ASP PHE TRP ARG LEU VAL TRP GLU GLN GLN SER SEQRES 10 A 291 HIS THR LEU VAL MET LEU THR ASN CYS MET GLU ALA GLY SEQRES 11 A 291 ARG VAL LYS CYS GLU HIS TYR TRP PRO LEU ASP SER GLN SEQRES 12 A 291 PRO CYS THR HIS GLY HIS LEU ARG VAL THR LEU VAL GLY SEQRES 13 A 291 GLU GLU VAL MET GLU ASN TRP THR VAL ARG GLU LEU LEU SEQRES 14 A 291 LEU LEU GLN VAL GLU GLU GLN LYS THR LEU SER VAL ARG SEQRES 15 A 291 GLN PHE HIS TYR GLN ALA TRP PRO ASP HIS GLY VAL PRO SEQRES 16 A 291 SER SER PRO ASP THR LEU LEU ALA PHE TRP ARG MET LEU SEQRES 17 A 291 ARG GLN TRP LEU ASP GLN THR MET GLU GLY GLY PRO PRO SEQRES 18 A 291 ILE VAL HIS SER SER ALA GLY VAL GLY ARG THR GLY THR SEQRES 19 A 291 LEU ILE ALA LEU ASP VAL LEU LEU ARG GLN LEU GLN SER SEQRES 20 A 291 GLU GLY LEU LEU GLY PRO PHE SER PHE VAL ARG LYS MET SEQRES 21 A 291 ARG GLU SER ARG PRO LEU MET VAL GLN THR GLU ALA GLN SEQRES 22 A 291 TYR VAL PHE LEU HIS GLN CYS ILE LEU ARG PHE LEU GLN SEQRES 23 A 291 GLN SER ALA GLN ALA HET PO4 A1101 5 HETNAM PO4 PHOSPHATE ION FORMUL 2 PO4 O4 P 3- FORMUL 3 HOH *189(H2 O) HELIX 1 AA1 ASP A 804 SER A 828 1 25 HELIX 2 AA2 ALA A 841 ASN A 848 5 8 HELIX 3 AA3 LEU A 896 GLN A 898 5 3 HELIX 4 AA4 THR A 899 GLN A 911 1 13 HELIX 5 AA5 SER A 992 ASP A 1008 1 17 HELIX 6 AA6 VAL A 1024 GLY A 1044 1 21 HELIX 7 AA7 GLY A 1047 ARG A 1059 1 13 HELIX 8 AA8 THR A 1065 SER A 1083 1 19 SHEET 1 AA1 2 ILE A 800 PRO A 801 0 SHEET 2 AA1 2 LEU A1045 LEU A1046 -1 O LEU A1046 N ILE A 800 SHEET 1 AA2 8 ALA A 877 MET A 880 0 SHEET 2 AA2 8 PHE A 889 THR A 892 -1 O PHE A 889 N MET A 880 SHEET 3 AA2 8 ILE A1017 HIS A1019 1 O VAL A1018 N ILE A 890 SHEET 4 AA2 8 THR A 914 MET A 917 1 N VAL A 916 O HIS A1019 SHEET 5 AA2 8 LYS A 972 TYR A 981 1 O PHE A 979 N LEU A 915 SHEET 6 AA2 8 TRP A 958 GLN A 967 -1 N LEU A 963 O VAL A 976 SHEET 7 AA2 8 LEU A 945 VAL A 954 -1 N VAL A 950 O GLU A 962 SHEET 8 AA2 8 CYS A 940 HIS A 942 -1 N CYS A 940 O VAL A 947 SHEET 1 AA3 2 MET A 922 GLU A 923 0 SHEET 2 AA3 2 ARG A 926 VAL A 927 -1 O ARG A 926 N GLU A 923 CRYST1 56.460 56.460 80.447 90.00 90.00 120.00 P 32 3 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 0.017712 0.010226 0.000000 0.00000 SCALE2 0.000000 0.020452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012431 0.00000