PDB Short entry for 2YD9 HEADER HYDROLASE 18-MAR-11 2YD9 TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-3 MODULE OF HUMAN RECEPTOR TITLE 2 PROTEIN TYROSINE PHOSPHATASE SIGMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG1-3, RESIDUES 30-321; COMPND 5 SYNONYM: R-PTP-S, RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA R- COMPND 6 PTP-SIGMA, RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA; 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 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PHLSEC KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.H.COLES,Y.SHEN,A.P.TENNEY,C.SIEBOLD,G.C.SUTTON,W.LU,J.T.GALLAGHER, AUTHOR 2 E.Y.JONES,J.G.FLANAGAN,A.R.ARICESCU REVDAT 4 20-DEC-23 2YD9 1 HETSYN REVDAT 3 29-JUL-20 2YD9 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 04-MAY-11 2YD9 1 REVDAT JRNL REMARK REVDAT 1 13-APR-11 2YD9 0 JRNL AUTH C.H.COLES,Y.SHEN,A.P.TENNEY,C.SIEBOLD,G.C.SUTTON,W.LU, JRNL AUTH 2 J.T.GALLAGHER,E.Y.JONES,J.G.FLANAGAN,A.R.ARICESCU JRNL TITL PROTEOGLYCAN-SPECIFIC MOLECULAR SWITCH FOR RPTP SIGMA JRNL TITL 2 CLUSTERING AND NEURONAL EXTENSION. JRNL REF SCIENCE V. 332 484 2011 JRNL REFN ISSN 0036-8075 JRNL PMID 21454754 JRNL DOI 10.1126/SCIENCE.1200840 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0077 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 13846 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) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 736 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1002 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3990 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.4440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2123 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 20 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.73000 REMARK 3 B22 (A**2) : -4.91000 REMARK 3 B33 (A**2) : 8.64000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.432 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.295 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.770 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2216 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1511 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3018 ; 0.974 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3660 ; 0.746 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 5.114 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;38.241 ;24.896 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 356 ;14.080 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;12.962 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 344 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2443 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 399 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 30 A 128 REMARK 3 ORIGIN FOR THE GROUP (A): -33.5113 -23.8646 -30.8818 REMARK 3 T TENSOR REMARK 3 T11: 0.9479 T22: 0.7281 REMARK 3 T33: 0.2164 T12: 0.1414 REMARK 3 T13: 0.0332 T23: -0.1411 REMARK 3 L TENSOR REMARK 3 L11: 6.0843 L22: 11.7653 REMARK 3 L33: 4.2762 L12: 0.7456 REMARK 3 L13: -1.4569 L23: -3.7735 REMARK 3 S TENSOR REMARK 3 S11: 0.2701 S12: 1.3959 S13: -0.3424 REMARK 3 S21: -1.7982 S22: -0.2016 S23: -0.6251 REMARK 3 S31: 0.3761 S32: 0.6187 S33: -0.0684 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 129 A 226 REMARK 3 ORIGIN FOR THE GROUP (A): -37.7439 -19.3642 -10.4949 REMARK 3 T TENSOR REMARK 3 T11: 0.1313 T22: 0.0812 REMARK 3 T33: 0.0624 T12: -0.0118 REMARK 3 T13: -0.0476 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 3.7401 L22: 6.4342 REMARK 3 L33: 1.7081 L12: -1.4780 REMARK 3 L13: -0.3912 L23: 0.6972 REMARK 3 S TENSOR REMARK 3 S11: 0.0853 S12: 0.2266 S13: 0.0620 REMARK 3 S21: -0.4527 S22: 0.0004 S23: -0.2486 REMARK 3 S31: 0.0841 S32: 0.0085 S33: -0.0857 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 227 A 314 REMARK 3 ORIGIN FOR THE GROUP (A): -64.4506 12.9783 8.9948 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.5464 REMARK 3 T33: 0.1508 T12: -0.1881 REMARK 3 T13: 0.0242 T23: -0.1145 REMARK 3 L TENSOR REMARK 3 L11: 14.4102 L22: 5.0306 REMARK 3 L33: 6.9837 L12: -4.9872 REMARK 3 L13: -5.0503 L23: 1.7081 REMARK 3 S TENSOR REMARK 3 S11: 0.2758 S12: -1.6584 S13: 0.3989 REMARK 3 S21: 0.8077 S22: -0.2224 S23: 0.0099 REMARK 3 S31: -0.4341 S32: -0.3371 S33: -0.0534 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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. CLEAR ELECTRON DENSITY WAS NOT VISIBLE FOR RESIDUES REMARK 3 68-74 AND THESE ARE NOT INCLUDED IN THE CRYSTAL STRUCTURE. REMARK 4 REMARK 4 2YD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1290047750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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 2YD4 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M SODIUM IODIDE, 0.1 REMARK 280 M BIS-TRIS PROPANE, PH 7.5 . REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.84950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.02150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 71.64150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.84950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.02150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 71.64150 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.84950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.02150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 71.64150 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.84950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.02150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.64150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.3 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 I IOD A1319 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 GLU A 27 REMARK 465 THR A 28 REMARK 465 GLY A 29 REMARK 465 LYS A 68 REMARK 465 LYS A 69 REMARK 465 GLY A 70 REMARK 465 LYS A 71 REMARK 465 LYS A 72 REMARK 465 VAL A 73 REMARK 465 ASN A 74 REMARK 465 VAL A 315 REMARK 465 LYS A 316 REMARK 465 SER A 317 REMARK 465 LEU A 318 REMARK 465 PRO A 319 REMARK 465 LYS A 320 REMARK 465 ALA A 321 REMARK 465 GLY A 322 REMARK 465 THR A 323 REMARK 465 LYS A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 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 54 109.71 -165.68 REMARK 500 SER A 86 -14.78 84.42 REMARK 500 LEU A 143 126.62 -39.10 REMARK 500 THR A 149 -9.21 75.38 REMARK 500 CYS A 156 113.01 -164.63 REMARK 500 ASN A 229 52.37 -145.01 REMARK 500 THR A 288 -76.70 -81.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FH7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PHOSPHATASE DOMAINS OF HUMAN PTPSIGMA REMARK 900 RELATED ID: 2YD1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF DROSOPHILA REMARK 900 RECEPTOR PROTEIN TYROSINE PHOSPHATASE DLAR REMARK 900 RELATED ID: 2YD2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE SIGMA REMARK 900 RELATED ID: 2YD3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE SIGMA REMARK 900 RELATED ID: 2YD4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF CHICKEN REMARK 900 RECEPTOR PROTEIN TYROSINE PHOSPHATASE SIGMA REMARK 900 RELATED ID: 2YD5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE LAR REMARK 900 RELATED ID: 2YD6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE DELTA REMARK 900 RELATED ID: 2YD7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE DELTA REMARK 900 RELATED ID: 2YD8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE N-TERMINAL IG1-2 MODULE OF HUMAN RECEPTOR REMARK 900 PROTEIN TYROSINE PHOSPHATASE LAR IN COMPLEX WITH SUCROSE REMARK 900 OCTASULPHATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- REMARK 999 TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM REMARK 999 THE PHLSEC VECTOR. THE R228Q AND R229N POINT MUTATIONS REMARK 999 WERE INTRODUCED TO PREVENT PROTEOLYTIC CLEAVAGE OF THE REMARK 999 PROTEIN. DBREF 2YD9 A 30 321 UNP Q13332 PTPRS_HUMAN 30 321 SEQADV 2YD9 GLU A 27 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 THR A 28 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 GLY A 29 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 GLN A 228 UNP Q13332 ARG 228 ENGINEERED MUTATION SEQADV 2YD9 ASN A 229 UNP Q13332 ARG 229 ENGINEERED MUTATION SEQADV 2YD9 GLY A 322 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 THR A 323 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 LYS A 324 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 325 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 326 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 327 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 328 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 329 UNP Q13332 EXPRESSION TAG SEQADV 2YD9 HIS A 330 UNP Q13332 EXPRESSION TAG SEQRES 1 A 304 GLU THR GLY GLU GLU PRO PRO ARG PHE ILE LYS GLU PRO SEQRES 2 A 304 LYS ASP GLN ILE GLY VAL SER GLY GLY VAL ALA SER PHE SEQRES 3 A 304 VAL CYS GLN ALA THR GLY ASP PRO LYS PRO ARG VAL THR SEQRES 4 A 304 TRP ASN LYS LYS GLY LYS LYS VAL ASN SER GLN ARG PHE SEQRES 5 A 304 GLU THR ILE GLU PHE ASP GLU SER ALA GLY ALA VAL LEU SEQRES 6 A 304 ARG ILE GLN PRO LEU ARG THR PRO ARG ASP GLU ASN VAL SEQRES 7 A 304 TYR GLU CYS VAL ALA GLN ASN SER VAL GLY GLU ILE THR SEQRES 8 A 304 VAL HIS ALA LYS LEU THR VAL LEU ARG GLU ASP GLN LEU SEQRES 9 A 304 PRO SER GLY PHE PRO ASN ILE ASP MET GLY PRO GLN LEU SEQRES 10 A 304 LYS VAL VAL GLU ARG THR ARG THR ALA THR MET LEU CYS SEQRES 11 A 304 ALA ALA SER GLY ASN PRO ASP PRO GLU ILE THR TRP PHE SEQRES 12 A 304 LYS ASP PHE LEU PRO VAL ASP PRO SER ALA SER ASN GLY SEQRES 13 A 304 ARG ILE LYS GLN LEU ARG SER GLY ALA LEU GLN ILE GLU SEQRES 14 A 304 SER SER GLU GLU THR ASP GLN GLY LYS TYR GLU CYS VAL SEQRES 15 A 304 ALA THR ASN SER ALA GLY VAL ARG TYR SER SER PRO ALA SEQRES 16 A 304 ASN LEU TYR VAL ARG VAL GLN ASN VAL ALA PRO ARG PHE SEQRES 17 A 304 SER ILE LEU PRO MET SER HIS GLU ILE MET PRO GLY GLY SEQRES 18 A 304 ASN VAL ASN ILE THR CYS VAL ALA VAL GLY SER PRO MET SEQRES 19 A 304 PRO TYR VAL LYS TRP MET GLN GLY ALA GLU ASP LEU THR SEQRES 20 A 304 PRO GLU ASP ASP MET PRO VAL GLY ARG ASN VAL LEU GLU SEQRES 21 A 304 LEU THR ASP VAL LYS ASP SER ALA ASN TYR THR CYS VAL SEQRES 22 A 304 ALA MET SER SER LEU GLY VAL ILE GLU ALA VAL ALA GLN SEQRES 23 A 304 ILE THR VAL LYS SER LEU PRO LYS ALA GLY THR LYS HIS SEQRES 24 A 304 HIS HIS HIS HIS HIS MODRES 2YD9 ASN A 250 ASN GLYCOSYLATION SITE MODRES 2YD9 ASN A 295 ASN GLYCOSYLATION SITE HET CL A1315 1 HET CL A1316 1 HET CL A1317 1 HET CL A1318 1 HET IOD A1319 1 HET IOD A1320 1 HET IOD A1321 1 HET IOD A1322 1 HET NAG A1323 14 HET NAG A1324 14 HET B3P A1325 19 HETNAM CL CHLORIDE ION HETNAM IOD IODIDE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 CL 4(CL 1-) FORMUL 6 IOD 4(I 1-) FORMUL 10 NAG 2(C8 H15 N O6) FORMUL 12 B3P C11 H26 N2 O6 FORMUL 13 HOH *20(H2 O) HELIX 1 1 ARG A 126 LEU A 130 5 5 HELIX 2 2 ASP A 176 ASN A 181 5 6 HELIX 3 3 GLU A 198 GLN A 202 5 5 SHEET 1 AA 4 ARG A 34 LYS A 37 0 SHEET 2 AA 4 ALA A 50 THR A 57 -1 O GLN A 55 N LYS A 37 SHEET 3 AA 4 GLY A 88 ILE A 93 -1 O ALA A 89 N CYS A 54 SHEET 4 AA 4 PHE A 78 PHE A 83 -1 O GLU A 79 N ARG A 92 SHEET 1 AB 4 GLN A 42 VAL A 45 0 SHEET 2 AB 4 HIS A 119 LEU A 125 1 O LYS A 121 N GLN A 42 SHEET 3 AB 4 VAL A 104 GLN A 110 -1 O TYR A 105 N ALA A 120 SHEET 4 AB 4 GLU A 115 ILE A 116 1 O ILE A 116 N ALA A 109 SHEET 1 AC 4 GLN A 42 VAL A 45 0 SHEET 2 AC 4 HIS A 119 LEU A 125 1 O LYS A 121 N GLN A 42 SHEET 3 AC 4 VAL A 104 GLN A 110 -1 O TYR A 105 N ALA A 120 SHEET 4 AC 4 ARG A 63 ASN A 67 -1 O ARG A 63 N GLN A 110 SHEET 1 AD 2 GLU A 115 ILE A 116 0 SHEET 2 AD 2 VAL A 104 GLN A 110 1 O ALA A 109 N ILE A 116 SHEET 1 AE 2 ASN A 136 MET A 139 0 SHEET 2 AE 2 ALA A 157 SER A 159 -1 O ALA A 157 N MET A 139 SHEET 1 AF 4 LYS A 144 GLU A 147 0 SHEET 2 AF 4 ALA A 221 ARG A 226 1 O ASN A 222 N LYS A 144 SHEET 3 AF 4 GLY A 203 ASN A 211 -1 O GLY A 203 N LEU A 223 SHEET 4 AF 4 GLY A 214 TYR A 217 1 O GLY A 214 N ASN A 211 SHEET 1 AG 5 LYS A 144 GLU A 147 0 SHEET 2 AG 5 ALA A 221 ARG A 226 1 O ASN A 222 N LYS A 144 SHEET 3 AG 5 GLY A 203 ASN A 211 -1 O GLY A 203 N LEU A 223 SHEET 4 AG 5 GLU A 165 LYS A 170 -1 O GLU A 165 N THR A 210 SHEET 5 AG 5 LEU A 173 PRO A 174 -1 O LEU A 173 N LYS A 170 SHEET 1 AH 2 GLY A 214 TYR A 217 0 SHEET 2 AH 2 GLY A 203 ASN A 211 1 O ALA A 209 N ARG A 216 SHEET 1 AI 3 ALA A 152 MET A 154 0 SHEET 2 AI 3 LEU A 192 ILE A 194 -1 O LEU A 192 N MET A 154 SHEET 3 AI 3 ILE A 184 GLN A 186 -1 O LYS A 185 N GLN A 193 SHEET 1 AJ 3 VAL A 230 ILE A 236 0 SHEET 2 AJ 3 VAL A 249 SER A 258 -1 O VAL A 254 N SER A 235 SHEET 3 AJ 3 ARG A 282 LEU A 287 -1 O ASN A 283 N CYS A 253 SHEET 1 AK 5 HIS A 241 GLU A 242 0 SHEET 2 AK 5 GLY A 305 THR A 314 1 O GLN A 312 N HIS A 241 SHEET 3 AK 5 ALA A 294 SER A 302 -1 O ALA A 294 N ILE A 313 SHEET 4 AK 5 TYR A 262 GLN A 267 -1 O TYR A 262 N MET A 301 SHEET 5 AK 5 GLU A 270 ASP A 271 -1 O GLU A 270 N GLN A 267 SSBOND 1 CYS A 54 CYS A 107 1555 1555 2.03 SSBOND 2 CYS A 156 CYS A 207 1555 1555 2.09 SSBOND 3 CYS A 253 CYS A 298 1555 1555 2.02 LINK ND2 ASN A 250 C1 NAG A1324 1555 1555 1.44 LINK ND2 ASN A 295 C1 NAG A1323 1555 1555 1.45 CISPEP 1 ASP A 59 PRO A 60 0 1.44 CISPEP 2 GLN A 94 PRO A 95 0 -9.56 CISPEP 3 THR A 98 PRO A 99 0 -0.06 CISPEP 4 ASN A 161 PRO A 162 0 -1.17 CISPEP 5 GLY A 246 GLY A 247 0 0.89 CISPEP 6 SER A 258 PRO A 259 0 6.10 CRYST1 71.699 90.043 143.283 90.00 90.00 90.00 I 2 2 2 8 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 0.013947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006979 0.00000