HEADER HYDROLASE 08-AUG-09 3A5J TITLE CRYSTAL STRUCTURE OF PROTEIN-TYROSINE PHOSPHATASE 1B COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-321; COMPND 5 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B, PTP-1B; COMPND 6 EC: 3.1.3.48; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ALPHA/BETA STRUCTURE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.ITO REVDAT 3 01-NOV-23 3A5J 1 REMARK SEQADV LINK REVDAT 2 11-OCT-17 3A5J 1 REMARK REVDAT 1 11-AUG-10 3A5J 0 JRNL AUTH N.IWAMOTO,S.ITO,D.SUMI,M.KOBAYASHI,T.KUMAGAI JRNL TITL POST-TRANSLATIONAL MODIFICATION OF A NON-CATALYTIC CYS121 OF JRNL TITL 2 PTP1B JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 34218 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1783 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2306 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.06000 REMARK 3 B12 (A**2) : -0.02000 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): 0.105 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.399 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2359 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3179 ; 2.180 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 281 ; 5.758 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;30.497 ;23.879 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 440 ;13.961 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.254 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1779 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1408 ; 1.338 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2281 ; 2.056 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 951 ; 3.318 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 898 ; 5.028 ; 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 : 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 1 A 15 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3611 7.3251 -11.0851 REMARK 3 T TENSOR REMARK 3 T11: 0.6075 T22: 0.4604 REMARK 3 T33: 0.6648 T12: 0.1217 REMARK 3 T13: -0.0539 T23: 0.0647 REMARK 3 L TENSOR REMARK 3 L11: 10.0683 L22: 4.8081 REMARK 3 L33: 9.3730 L12: 1.6468 REMARK 3 L13: -8.1816 L23: 0.6392 REMARK 3 S TENSOR REMARK 3 S11: 0.2463 S12: -0.3034 S13: 0.6473 REMARK 3 S21: 0.6499 S22: -0.1542 S23: 0.6164 REMARK 3 S31: -0.8973 S32: -0.2448 S33: -0.0921 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 16 A 234 REMARK 3 ORIGIN FOR THE GROUP (A): 30.4228 -17.8070 -3.5536 REMARK 3 T TENSOR REMARK 3 T11: 0.1238 T22: 0.0974 REMARK 3 T33: 0.0247 T12: -0.0259 REMARK 3 T13: -0.0200 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 1.6269 L22: 2.0507 REMARK 3 L33: 0.7792 L12: 0.4480 REMARK 3 L13: 0.0471 L23: -0.0976 REMARK 3 S TENSOR REMARK 3 S11: -0.0289 S12: 0.0067 S13: 0.0703 REMARK 3 S21: -0.1037 S22: 0.0270 S23: 0.2182 REMARK 3 S31: -0.0196 S32: -0.0726 S33: 0.0020 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 235 A 282 REMARK 3 ORIGIN FOR THE GROUP (A): 21.8398 -0.6302 -4.0283 REMARK 3 T TENSOR REMARK 3 T11: 0.2118 T22: 0.2101 REMARK 3 T33: 0.2944 T12: 0.0017 REMARK 3 T13: -0.0444 T23: -0.0266 REMARK 3 L TENSOR REMARK 3 L11: 4.5960 L22: 2.8100 REMARK 3 L33: 1.2243 L12: -0.2586 REMARK 3 L13: 1.4022 L23: -0.4618 REMARK 3 S TENSOR REMARK 3 S11: -0.0758 S12: -0.3343 S13: 0.3513 REMARK 3 S21: 0.0683 S22: 0.0193 S23: 0.8035 REMARK 3 S31: -0.2030 S32: -0.4303 S33: 0.0565 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 : 1.40 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 U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3A5J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000028837. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36101 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.750 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: PDB ENTRY 2CMA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 48.31133 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 24.15567 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.15567 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.31133 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 -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 GLY A 283 REMARK 465 ASP A 284 REMARK 465 SER A 285 REMARK 465 SER A 286 REMARK 465 VAL A 287 REMARK 465 GLN A 288 REMARK 465 ASP A 289 REMARK 465 GLN A 290 REMARK 465 TRP A 291 REMARK 465 LYS A 292 REMARK 465 GLU A 293 REMARK 465 LEU A 294 REMARK 465 SER A 295 REMARK 465 HIS A 296 REMARK 465 GLU A 297 REMARK 465 ASP A 298 REMARK 465 LEU A 299 REMARK 465 GLU A 300 REMARK 465 PRO A 301 REMARK 465 PRO A 302 REMARK 465 PRO A 303 REMARK 465 GLU A 304 REMARK 465 HIS A 305 REMARK 465 ILE A 306 REMARK 465 PRO A 307 REMARK 465 PRO A 308 REMARK 465 PRO A 309 REMARK 465 PRO A 310 REMARK 465 ARG A 311 REMARK 465 PRO A 312 REMARK 465 PRO A 313 REMARK 465 LYS A 314 REMARK 465 ARG A 315 REMARK 465 ILE A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 PRO A 319 REMARK 465 HIS A 320 REMARK 465 ASN A 321 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 O GLU A 2 N GLU A 6 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 47 CB ARG A 47 CG -0.186 REMARK 500 VAL A 108 CB VAL A 108 CG1 0.139 REMARK 500 CYS A 121 CB CYS A 121 SG -0.166 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 ASP A 22 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 48 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 LEU A 88 CB - CG - CD2 ANGL. DEV. = -11.1 DEGREES REMARK 500 ASP A 137 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 257 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 ASP A 63 -102.44 -156.04 REMARK 500 LYS A 131 73.03 -119.98 REMARK 500 CYS A 215 -134.73 -136.65 REMARK 500 ILE A 261 111.21 73.62 REMARK 500 ILE A 281 31.29 -82.57 REMARK 500 REMARK 500 REMARK: NULL 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 MG A 322 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 390 O REMARK 620 2 HOH A 459 O 89.7 REMARK 620 3 HOH A 519 O 174.9 92.5 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 MG A 322 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A5K RELATED DB: PDB DBREF 3A5J A 2 321 UNP P18031 PTN1_HUMAN 2 321 SEQADV 3A5J MET A -5 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A -4 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A -3 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A -2 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A -1 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A 0 UNP P18031 EXPRESSION TAG SEQADV 3A5J HIS A 1 UNP P18031 EXPRESSION TAG SEQRES 1 A 327 MET HIS HIS HIS HIS HIS HIS GLU MET GLU LYS GLU PHE SEQRES 2 A 327 GLU GLN ILE ASP LYS SER GLY SER TRP ALA ALA ILE TYR SEQRES 3 A 327 GLN ASP ILE ARG HIS GLU ALA SER ASP PHE PRO CYS ARG SEQRES 4 A 327 VAL ALA LYS LEU PRO LYS ASN LYS ASN ARG ASN ARG TYR SEQRES 5 A 327 ARG ASP VAL SER PRO PHE ASP HIS SER ARG ILE LYS LEU SEQRES 6 A 327 HIS GLN GLU ASP ASN ASP TYR ILE ASN ALA SER LEU ILE SEQRES 7 A 327 LYS MET GLU GLU ALA GLN ARG SER TYR ILE LEU THR GLN SEQRES 8 A 327 GLY PRO LEU PRO ASN THR CYS GLY HIS PHE TRP GLU MET SEQRES 9 A 327 VAL TRP GLU GLN LYS SER ARG GLY VAL VAL MET LEU ASN SEQRES 10 A 327 ARG VAL MET GLU LYS GLY SER LEU LYS CYS ALA GLN TYR SEQRES 11 A 327 TRP PRO GLN LYS GLU GLU LYS GLU MET ILE PHE GLU ASP SEQRES 12 A 327 THR ASN LEU LYS LEU THR LEU ILE SER GLU ASP ILE LYS SEQRES 13 A 327 SER TYR TYR THR VAL ARG GLN LEU GLU LEU GLU ASN LEU SEQRES 14 A 327 THR THR GLN GLU THR ARG GLU ILE LEU HIS PHE HIS TYR SEQRES 15 A 327 THR THR TRP PRO ASP PHE GLY VAL PRO GLU SER PRO ALA SEQRES 16 A 327 SER PHE LEU ASN PHE LEU PHE LYS VAL ARG GLU SER GLY SEQRES 17 A 327 SER LEU SER PRO GLU HIS GLY PRO VAL VAL VAL HIS CYS SEQRES 18 A 327 SER ALA GLY ILE GLY ARG SER GLY THR PHE CYS LEU ALA SEQRES 19 A 327 ASP THR CYS LEU LEU LEU MET ASP LYS ARG LYS ASP PRO SEQRES 20 A 327 SER SER VAL ASP ILE LYS LYS VAL LEU LEU GLU MET ARG SEQRES 21 A 327 LYS PHE ARG MET GLY LEU ILE GLN THR ALA ASP GLN LEU SEQRES 22 A 327 ARG PHE SER TYR LEU ALA VAL ILE GLU GLY ALA LYS PHE SEQRES 23 A 327 ILE MET GLY ASP SER SER VAL GLN ASP GLN TRP LYS GLU SEQRES 24 A 327 LEU SER HIS GLU ASP LEU GLU PRO PRO PRO GLU HIS ILE SEQRES 25 A 327 PRO PRO PRO PRO ARG PRO PRO LYS ARG ILE LEU GLU PRO SEQRES 26 A 327 HIS ASN HET MG A 322 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *200(H2 O) HELIX 1 1 GLU A 2 GLY A 14 1 13 HELIX 2 2 SER A 15 ALA A 27 1 13 HELIX 3 3 CYS A 32 LEU A 37 1 6 HELIX 4 4 PRO A 38 ASN A 44 5 7 HELIX 5 5 THR A 91 LYS A 103 1 13 HELIX 6 6 PRO A 188 GLY A 202 1 15 HELIX 7 7 GLY A 220 ARG A 238 1 19 HELIX 8 8 ASP A 240 VAL A 244 5 5 HELIX 9 9 ASP A 245 ARG A 254 1 10 HELIX 10 10 THR A 263 ILE A 281 1 19 SHEET 1 A 9 ARG A 56 LYS A 58 0 SHEET 2 A 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57 SHEET 3 A 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72 SHEET 4 A 9 VAL A 211 HIS A 214 1 O VAL A 213 N ILE A 82 SHEET 5 A 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212 SHEET 6 A 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 A 9 TYR A 153 ASN A 162 -1 N THR A 154 O HIS A 175 SHEET 8 A 9 LEU A 140 ILE A 149 -1 N LYS A 141 O GLU A 161 SHEET 9 A 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140 SHEET 1 B 2 MET A 114 GLU A 115 0 SHEET 2 B 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115 LINK MG MG A 322 O HOH A 390 1555 1555 1.95 LINK MG MG A 322 O HOH A 459 1555 1555 1.99 LINK MG MG A 322 O HOH A 519 1555 1555 1.95 SITE 1 AC1 4 HOH A 390 HOH A 459 HOH A 466 HOH A 519 CRYST1 88.426 88.426 72.467 90.00 90.00 120.00 P 32 2 1 6 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 0.011309 0.006529 0.000000 0.00000 SCALE2 0.000000 0.013058 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013799 0.00000