HEADER HYDROLASE 23-FEB-06 2CFV TITLE CRYSTAL STRUCTURE OF HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE TITLE 2 J COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE J; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1019-1311; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE ETA, R-PTP-ETA, HPTP ETA, COMPND 6 PROTEIN-TYROSINE PHOSPHATASE RECEPTOR TYPE J, DENSITY-ENHANCED COMPND 7 PHOSPHATASE 1, DEP-1, CD14 8 ANTIGEN; COMPND 8 EC: 3.1.3.48; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PNIC28-BSA4 KEYWDS HYDROLASE, RECEPTOR TYPE TYROSINE PHOSPHATASE J, PTPRJ, GLYCOPROTEIN, KEYWDS 2 PROTEIN PHOSPHATASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.DEBRECZENI,A.J.BARR,J.ESWARAN,E.UGOCHUKWU,M.SUNDSTROM,J.WEIGELT, AUTHOR 2 C.ARROWSMITH,A.EDWARDS,S.KNAPP REVDAT 6 13-DEC-23 2CFV 1 REMARK LINK REVDAT 5 08-MAY-19 2CFV 1 REMARK REVDAT 4 20-JUN-12 2CFV 1 JRNL REMARK REVDAT 3 13-JUL-11 2CFV 1 VERSN REVDAT 2 03-FEB-09 2CFV 1 VERSN SOURCE AUTHOR JRNL REVDAT 2 2 1 REMARK SITE REVDAT 1 09-MAR-06 2CFV 0 JRNL AUTH A.J.BARR,E.UGOCHUKWU,W.H.LEE,O.N.F.KING,P.FILIPPAKOPOULOS, JRNL AUTH 2 I.ALFANO,P.SAVITSKY,N.A.BURGESS-BROWN,S.MULLER,S.KNAPP JRNL TITL LARGE-SCALE STRUCTURAL ANALYSIS OF THE CLASSICAL HUMAN JRNL TITL 2 PROTEIN TYROSINE PHOSPHATOME. JRNL REF CELL(CAMBRIDGE,MASS.) V. 136 352 2009 JRNL REFN ISSN 0092-8674 JRNL PMID 19167335 JRNL DOI 10.1016/J.CELL.2008.11.038 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 547 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 788 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2130 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : 1.23000 REMARK 3 B33 (A**2) : -1.85000 REMARK 3 B12 (A**2) : 0.62000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.513 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.285 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.803 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2193 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1418 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2979 ; 1.296 ; 1.926 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3440 ; 0.915 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 264 ; 6.914 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;37.141 ;23.832 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 342 ;16.956 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;18.465 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 333 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2441 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 467 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 464 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1358 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1049 ; 0.190 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1101 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 58 ; 0.155 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.245 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.170 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.163 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1374 ; 0.485 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2159 ; 0.846 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 947 ; 1.148 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 820 ; 1.683 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -19 A 1301 REMARK 3 ORIGIN FOR THE GROUP (A): -7.0540 28.5200 -14.3810 REMARK 3 T TENSOR REMARK 3 T11: 0.2010 T22: -0.1333 REMARK 3 T33: -0.0929 T12: -0.1140 REMARK 3 T13: 0.0393 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 1.7566 L22: 3.2916 REMARK 3 L33: 3.5090 L12: -0.4098 REMARK 3 L13: -0.0498 L23: -0.7789 REMARK 3 S TENSOR REMARK 3 S11: -0.1634 S12: -0.0701 S13: -0.2750 REMARK 3 S21: 0.2248 S22: 0.1076 S23: 0.2215 REMARK 3 S31: 0.8140 S32: -0.3864 S33: 0.0558 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2CFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1290027927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA 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 : SI REMARK 200 OPTICS : MIRROS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.760 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.13 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.180 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: PDB ENTRY 2AHS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M NICL2,0.1M TRIS PH 8.5, 1M REMARK 280 LI2SO4,150 UL SITTING DROPS, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.03000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.84338 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.84667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 43.03000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 24.84338 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.84667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 43.03000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 24.84338 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.84667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.68676 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 79.69333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 49.68676 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 79.69333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 49.68676 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 79.69333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -212.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 -43.03000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 74.53015 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 43.03000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 74.53015 REMARK 350 BIOMT3 3 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 -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 LYS A 1140 REMARK 465 CYS A 1141 REMARK 465 VAL A 1142 REMARK 465 GLU A 1143 REMARK 465 GLN A 1144 REMARK 465 GLY A 1145 REMARK 465 ARG A 1146 REMARK 465 THR A 1147 REMARK 465 LYS A 1148 REMARK 465 CYS A 1149 REMARK 465 GLU A 1150 REMARK 465 LYS A 1156 REMARK 465 GLN A 1157 REMARK 465 PRO A 1175 REMARK 465 GLU A 1176 REMARK 465 THR A 1189 REMARK 465 SER A 1190 REMARK 465 SER A 1202 REMARK 465 ALA A 1203 REMARK 465 PRO A 1204 REMARK 465 ASP A 1205 REMARK 465 HIS A 1206 REMARK 465 GLY A 1207 REMARK 465 VAL A 1208 REMARK 465 PRO A 1209 REMARK 465 ASP A 1210 REMARK 465 MET A 1226 REMARK 465 LYS A 1227 REMARK 465 GLN A 1228 REMARK 465 SER A 1229 REMARK 465 PRO A 1230 REMARK 465 PRO A 1231 REMARK 465 GLU A 1232 REMARK 465 SER A 1233 REMARK 465 SER A 1301 REMARK 465 GLN A 1302 REMARK 465 LYS A 1303 REMARK 465 ASP A 1304 REMARK 465 SER A 1305 REMARK 465 LYS A 1306 REMARK 465 VAL A 1307 REMARK 465 ASP A 1308 REMARK 465 LEU A 1309 REMARK 465 ILE A 1310 REMARK 465 TYR A 1311 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 ASN A -6 CG OD1 ND2 REMARK 470 PHE A -3 CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A -2 CG CD OE1 NE2 REMARK 470 LYS A1019 CE NZ REMARK 470 ARG A1022 NE CZ NH1 NH2 REMARK 470 GLU A1027 CG CD OE1 OE2 REMARK 470 LYS A1031 CG CD CE NZ REMARK 470 LYS A1032 CE NZ REMARK 470 GLN A1034 CD OE1 NE2 REMARK 470 ASP A1036 CG OD1 OD2 REMARK 470 SER A1037 OG REMARK 470 GLU A1043 CD OE1 OE2 REMARK 470 GLU A1046 CD OE1 OE2 REMARK 470 LYS A1049 CD CE NZ REMARK 470 ARG A1066 CG CD NE CZ NH1 NH2 REMARK 470 LEU A1120 CG CD1 CD2 REMARK 470 LYS A1121 CE NZ REMARK 470 TYR A1133 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A1185 CG CD CE NZ REMARK 470 ILE A1187 CG1 CG2 CD1 REMARK 470 GLU A1191 CG CD OE1 OE2 REMARK 470 LEU A1214 CG CD1 CD2 REMARK 470 ASP A1224 CG OD1 OD2 REMARK 470 ILE A1298 CG1 CG2 CD1 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 MET A 0 142.24 -174.23 REMARK 500 SER A1037 74.94 54.30 REMARK 500 GLN A1087 -62.19 -154.15 REMARK 500 ASN A1096 84.02 -69.28 REMARK 500 CYS A1239 -118.67 -113.58 REMARK 500 VAL A1243 -57.89 -140.09 REMARK 500 VAL A1282 95.32 57.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 1224 TYR A 1225 -147.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2005 DISTANCE = 7.47 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A2303 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -19 NE2 REMARK 620 2 HIS A -17 NE2 94.7 REMARK 620 3 LYS A1106 NZ 78.2 164.0 REMARK 620 4 HIS A1277 NE2 160.5 91.7 90.8 REMARK 620 5 HOH A2019 O 72.8 86.1 78.1 89.3 REMARK 620 6 CL A2304 CL 84.7 86.6 106.8 114.1 155.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A2302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -18 NE2 REMARK 620 2 HIS A -18 NE2 89.5 REMARK 620 3 HIS A -18 NE2 96.0 83.4 REMARK 620 4 HIS A -16 NE2 97.8 84.6 161.5 REMARK 620 5 HIS A -16 NE2 168.9 79.5 84.0 80.0 REMARK 620 6 HIS A -16 NE2 106.3 164.1 96.0 91.8 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A2305 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2005 O REMARK 620 2 HOH A2005 O 18.7 REMARK 620 3 HOH A2005 O 18.3 18.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 2304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 2306 DBREF 2CFV A -22 0 PDB 2CFV 2CFV -22 0 DBREF 2CFV A 1019 1311 UNP Q12913 PTPRJ_HUMAN 1019 1311 SEQRES 1 A 316 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 316 GLY THR GLU ASN LEU TYR PHE GLN SER MET LYS LEU ILE SEQRES 3 A 316 ARG VAL GLU ASN PHE GLU ALA TYR PHE LYS LYS GLN GLN SEQRES 4 A 316 ALA ASP SER ASN CYS GLY PHE ALA GLU GLU TYR GLU ASP SEQRES 5 A 316 LEU LYS LEU VAL GLY ILE SER GLN PRO LYS TYR ALA ALA SEQRES 6 A 316 GLU LEU ALA GLU ASN ARG GLY LYS ASN ARG TYR ASN ASN SEQRES 7 A 316 VAL LEU PRO TYR ASP ILE SER ARG VAL LYS LEU SER VAL SEQRES 8 A 316 GLN THR HIS SER THR ASP ASP TYR ILE ASN ALA ASN TYR SEQRES 9 A 316 MET PRO GLY TYR HIS SER LYS LYS ASP PHE ILE ALA THR SEQRES 10 A 316 GLN GLY PRO LEU PRO ASN THR LEU LYS ASP PHE TRP ARG SEQRES 11 A 316 MET VAL TRP GLU LYS ASN VAL TYR ALA ILE ILE MET LEU SEQRES 12 A 316 THR LYS CYS VAL GLU GLN GLY ARG THR LYS CYS GLU GLU SEQRES 13 A 316 TYR TRP PRO SER LYS GLN ALA GLN ASP TYR GLY ASP ILE SEQRES 14 A 316 THR VAL ALA MET THR SER GLU ILE VAL LEU PRO GLU TRP SEQRES 15 A 316 THR ILE ARG ASP PHE THR VAL LYS ASN ILE GLN THR SER SEQRES 16 A 316 GLU SER HIS PRO LEU ARG GLN PHE HIS PHE THR SER ALA SEQRES 17 A 316 PRO ASP HIS GLY VAL PRO ASP THR THR ASP LEU LEU ILE SEQRES 18 A 316 ASN PHE ARG TYR LEU VAL ARG ASP TYR MET LYS GLN SER SEQRES 19 A 316 PRO PRO GLU SER PRO ILE LEU VAL HIS CYS SER ALA GLY SEQRES 20 A 316 VAL GLY ARG THR GLY THR PHE ILE ALA ILE ASP ARG LEU SEQRES 21 A 316 ILE TYR GLN ILE GLU ASN GLU ASN THR VAL ASP VAL TYR SEQRES 22 A 316 GLY ILE VAL TYR ASP LEU ARG MET HIS ARG PRO LEU MET SEQRES 23 A 316 VAL GLN THR GLU ASP GLN TYR VAL PHE LEU ASN GLN CYS SEQRES 24 A 316 VAL LEU ASP ILE VAL ARG SER GLN LYS ASP SER LYS VAL SEQRES 25 A 316 ASP LEU ILE TYR HET NI A2302 1 HET NI A2303 1 HET CL A2304 1 HET NI A2305 1 HET NI A2306 1 HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION FORMUL 2 NI 4(NI 2+) FORMUL 4 CL CL 1- FORMUL 7 HOH *25(H2 O) HELIX 1 1 ASP A -11 GLN A -2 1 10 HELIX 2 2 ASN A 1025 GLN A 1034 1 10 HELIX 3 3 ASN A 1038 LEU A 1048 1 11 HELIX 4 4 LYS A 1049 VAL A 1051 5 3 HELIX 5 5 LYS A 1057 LEU A 1062 1 6 HELIX 6 6 ALA A 1063 ASN A 1069 5 7 HELIX 7 7 TYR A 1077 SER A 1080 5 4 HELIX 8 8 HIS A 1089 TYR A 1094 5 6 HELIX 9 9 LEU A 1116 ASN A 1118 5 3 HELIX 10 10 THR A 1119 LYS A 1130 1 12 HELIX 11 11 THR A 1212 ARG A 1223 1 12 HELIX 12 12 VAL A 1243 GLU A 1262 1 20 HELIX 13 13 ASP A 1266 MET A 1276 1 11 HELIX 14 14 THR A 1284 VAL A 1299 1 16 SHEET 1 AA 2 ILE A1021 ARG A1022 0 SHEET 2 AA 2 THR A1264 VAL A1265 -1 O VAL A1265 N ILE A1021 SHEET 1 AB 8 ALA A1097 MET A1100 0 SHEET 2 AB 8 PHE A1109 THR A1112 -1 O PHE A1109 N MET A1100 SHEET 3 AB 8 ILE A1235 HIS A1238 1 O ILE A1235 N ILE A1110 SHEET 4 AB 8 ALA A1134 MET A1137 1 O ALA A1134 N LEU A1236 SHEET 5 AB 8 SER A1192 HIS A1199 1 O ARG A1196 N ILE A1135 SHEET 6 AB 8 THR A1178 ASN A1186 -1 O THR A1178 N HIS A1199 SHEET 7 AB 8 ILE A1164 VAL A1173 -1 O THR A1165 N LYS A1185 SHEET 8 AB 8 GLN A1159 TYR A1161 -1 O GLN A1159 N VAL A1166 LINK NE2 HIS A -19 NI NI A2303 2665 1555 2.26 LINK NE2 HIS A -18 NI NI A2302 1555 1555 1.97 LINK NE2 HIS A -18 NI NI A2302 2665 1555 2.47 LINK NE2 HIS A -18 NI NI A2302 3565 1555 2.26 LINK NE2 HIS A -17 NI NI A2303 2665 1555 2.17 LINK NE2 HIS A -16 NI NI A2302 1555 1555 2.19 LINK NE2 HIS A -16 NI NI A2302 2665 1555 2.44 LINK NE2 HIS A -16 NI NI A2302 3565 1555 1.96 LINK NZ LYS A1106 NI NI A2303 1555 1555 1.83 LINK NE2 HIS A1277 NI NI A2303 1555 1555 2.21 LINK O HOH A2004 NI NI A2306 1555 1555 2.38 LINK O HOH A2005 NI NI A2305 2665 1555 2.54 LINK O HOH A2005 NI NI A2305 3565 1555 2.51 LINK O HOH A2005 NI NI A2305 1555 1555 2.60 LINK O HOH A2019 NI NI A2303 1555 1555 1.96 LINK NI NI A2303 CL CL A2304 1555 1555 2.36 SITE 1 AC1 2 HIS A -16 HIS A -18 SITE 1 AC2 6 HIS A -17 HIS A -19 LYS A1106 HIS A1277 SITE 2 AC2 6 HOH A2019 CL A2304 SITE 1 AC3 4 HIS A -17 HIS A -19 LYS A1106 NI A2303 SITE 1 AC4 2 HOH A2002 HOH A2005 SITE 1 AC5 3 HIS A -19 HOH A2003 HOH A2004 CRYST1 86.060 86.060 119.540 90.00 90.00 120.00 H 3 9 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 0.011620 0.006709 0.000000 0.00000 SCALE2 0.000000 0.013417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008365 0.00000