HEADER HYDROLASE 14-FEB-23 8G65 TITLE WILDTYPE PTP1B IN COMPLEX WITH DES4799 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROTEIN-TYROSINE PHOSPHATASE 1B,PTP-1B; COMPND 5 EC: 3.1.3.48; COMPND 6 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: PTPN1, PTP1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.GREISMAN,L.WILLMORE,C.Y.YEH,F.GIORDANETTO,S.SHAHAMADTAR, AUTHOR 2 H.NISONOFF,P.MARAGAKIS,D.E.SHAW REVDAT 3 17-MAY-23 8G65 1 JRNL REVDAT 2 03-MAY-23 8G65 1 JRNL REVDAT 1 26-APR-23 8G65 0 JRNL AUTH J.B.GREISMAN,L.WILLMORE,C.Y.YEH,F.GIORDANETTO,S.SHAHAMADTAR, JRNL AUTH 2 H.NISONOFF,P.MARAGAKIS,D.E.SHAW JRNL TITL DISCOVERY AND VALIDATION OF THE BINDING POSES OF ALLOSTERIC JRNL TITL 2 FRAGMENT HITS TO PROTEIN TYROSINE PHOSPHATASE 1B: FROM JRNL TITL 3 MOLECULAR DYNAMICS SIMULATIONS TO X-RAY CRYSTALLOGRAPHY. JRNL REF J.CHEM.INF.MODEL. V. 63 2644 2023 JRNL REFN ESSN 1549-960X JRNL PMID 37086179 JRNL DOI 10.1021/ACS.JCIM.3C00236 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 113016 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) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6003 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8182 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2600 REMARK 3 BIN FREE R VALUE SET COUNT : 488 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4751 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 642 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.88000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -1.77000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.062 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.215 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5086 ; 0.030 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4835 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6905 ; 2.375 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11219 ; 1.264 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 647 ; 5.948 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 251 ;34.922 ;24.223 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 970 ;14.229 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;20.331 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 736 ; 0.157 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5801 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1198 ; 0.005 ; 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): 2394 ; 3.416 ; 1.949 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2393 ; 3.416 ; 1.948 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3006 ; 4.056 ; 2.943 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3007 ; 4.055 ; 2.943 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2691 ; 5.333 ; 2.465 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2692 ; 5.332 ; 2.465 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3866 ; 6.269 ; 3.496 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5990 ; 6.191 ;17.855 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5991 ; 6.190 ;17.856 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 9920 ; 5.364 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 208 ;29.270 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 10214 ;19.291 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 8G65 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000270403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92819 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 119149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 82.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 1.70600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: IN-HOUSE STRUCTURE OF SAME PROTEIN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR SOLUTION: 50 MM MES (PH REMARK 280 6.2), 14% PEG6000, 50 MM MGCL2; PROTEIN SOLUTION: 10.3 MG/ML PTP- REMARK 280 1B 1-298 IN 25 MM HEPES PH 7.2, 150 MM NACL, 1 MM EDTA, 2 MM DTT, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 82.88000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.72000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 124.32000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.72000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.44000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.72000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 124.32000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.72000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.72000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.44000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.88000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 HOH A 559 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 SER B 285 REMARK 465 SER B 286 REMARK 465 VAL B 287 REMARK 465 GLN B 288 REMARK 465 ASP B 289 REMARK 465 GLN B 290 REMARK 465 TRP B 291 REMARK 465 LYS B 292 REMARK 465 GLU B 293 REMARK 465 LEU B 294 REMARK 465 SER B 295 REMARK 465 HIS B 296 REMARK 465 GLU B 297 REMARK 465 ASP B 298 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 OD2 ASP A 289 NZ LYS B 103 2.15 REMARK 500 O HOH A 680 O HOH A 697 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 445 O HOH A 688 6555 2.18 REMARK 500 CE MET A 1 O HOH B 447 6445 2.19 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 CYS A 121 CB CYS A 121 SG -0.180 REMARK 500 GLU A 147 CD GLU A 147 OE1 -0.094 REMARK 500 TYR A 153 CG TYR A 153 CD2 0.082 REMARK 500 TYR A 153 CE1 TYR A 153 CZ 0.087 REMARK 500 TRP A 291 CB TRP A 291 CG 0.143 REMARK 500 GLU A 297 CD GLU A 297 OE1 0.097 REMARK 500 ASP A 298 C ASP A 298 OXT 0.129 REMARK 500 GLU B 2 CD GLU B 2 OE1 0.137 REMARK 500 GLU B 2 CD GLU B 2 OE2 0.078 REMARK 500 GLU B 6 CD GLU B 6 OE2 0.067 REMARK 500 GLU B 132 CD GLU B 132 OE1 0.078 REMARK 500 GLU B 147 CB GLU B 147 CG -0.123 REMARK 500 GLU B 147 CD GLU B 147 OE2 -0.074 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. = 5.8 DEGREES REMARK 500 ASP A 22 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 CYS A 121 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 CYS A 121 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP A 137 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 MET A 253 CG - SD - CE ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 268 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU A 276 OE1 - CD - OE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 MET B 1 CG - SD - CE ANGL. DEV. = 10.8 DEGREES REMARK 500 PHE B 30 CB - CG - CD2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG B 79 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG B 79 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 112 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 112 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG B 199 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 CYS B 215 CB - CA - C ANGL. DEV. = 10.0 DEGREES REMARK 500 MET B 235 CG - SD - CE ANGL. DEV. = -15.6 DEGREES REMARK 500 ASP B 236 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP B 245 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG B 257 NH1 - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG B 257 NE - CZ - NH1 ANGL. DEV. = 5.0 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 63 167.77 150.92 REMARK 500 ASN A 64 124.99 -35.73 REMARK 500 CYS A 215 -133.72 -127.07 REMARK 500 ILE A 219 -33.52 -136.01 REMARK 500 ILE A 261 106.16 74.51 REMARK 500 LYS B 116 76.45 39.93 REMARK 500 CYS B 215 -132.01 -131.08 REMARK 500 ILE B 219 -31.82 -134.54 REMARK 500 ILE B 261 112.17 78.08 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 A 722 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 723 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B 716 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 717 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH B 718 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH B 719 DISTANCE = 6.56 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 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 435 O REMARK 620 2 HOH B 483 O 94.3 REMARK 620 3 HOH B 659 O 89.5 89.5 REMARK 620 4 HOH B 673 O 171.4 77.4 92.5 REMARK 620 5 HOH B 679 O 95.3 168.1 97.6 92.7 REMARK 620 6 HOH B 688 O 111.8 101.5 154.8 68.4 68.3 REMARK 620 N 1 2 3 4 5 DBREF 8G65 A 1 298 UNP P18031 PTN1_HUMAN 1 298 DBREF 8G65 B 1 298 UNP P18031 PTN1_HUMAN 1 298 SEQRES 1 A 298 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER SEQRES 2 A 298 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU SEQRES 3 A 298 ALA SER ASP PHE PRO CYS ARG VAL ALA LYS LEU PRO LYS SEQRES 4 A 298 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE SEQRES 5 A 298 ASP HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP SEQRES 6 A 298 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN SEQRES 7 A 298 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR SEQRES 8 A 298 CYS GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER SEQRES 9 A 298 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SEQRES 10 A 298 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU SEQRES 11 A 298 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR SEQRES 12 A 298 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG SEQRES 13 A 298 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG SEQRES 14 A 298 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP PHE SEQRES 15 A 298 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU SEQRES 16 A 298 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS SEQRES 17 A 298 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG SEQRES 18 A 298 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU SEQRES 19 A 298 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS SEQRES 20 A 298 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU SEQRES 21 A 298 ILE GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA SEQRES 22 A 298 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER SEQRES 23 A 298 VAL GLN ASP GLN TRP LYS GLU LEU SER HIS GLU ASP SEQRES 1 B 298 MET GLU MET GLU LYS GLU PHE GLU GLN ILE ASP LYS SER SEQRES 2 B 298 GLY SER TRP ALA ALA ILE TYR GLN ASP ILE ARG HIS GLU SEQRES 3 B 298 ALA SER ASP PHE PRO CYS ARG VAL ALA LYS LEU PRO LYS SEQRES 4 B 298 ASN LYS ASN ARG ASN ARG TYR ARG ASP VAL SER PRO PHE SEQRES 5 B 298 ASP HIS SER ARG ILE LYS LEU HIS GLN GLU ASP ASN ASP SEQRES 6 B 298 TYR ILE ASN ALA SER LEU ILE LYS MET GLU GLU ALA GLN SEQRES 7 B 298 ARG SER TYR ILE LEU THR GLN GLY PRO LEU PRO ASN THR SEQRES 8 B 298 CYS GLY HIS PHE TRP GLU MET VAL TRP GLU GLN LYS SER SEQRES 9 B 298 ARG GLY VAL VAL MET LEU ASN ARG VAL MET GLU LYS GLY SEQRES 10 B 298 SER LEU LYS CYS ALA GLN TYR TRP PRO GLN LYS GLU GLU SEQRES 11 B 298 LYS GLU MET ILE PHE GLU ASP THR ASN LEU LYS LEU THR SEQRES 12 B 298 LEU ILE SER GLU ASP ILE LYS SER TYR TYR THR VAL ARG SEQRES 13 B 298 GLN LEU GLU LEU GLU ASN LEU THR THR GLN GLU THR ARG SEQRES 14 B 298 GLU ILE LEU HIS PHE HIS TYR THR THR TRP PRO ASP PHE SEQRES 15 B 298 GLY VAL PRO GLU SER PRO ALA SER PHE LEU ASN PHE LEU SEQRES 16 B 298 PHE LYS VAL ARG GLU SER GLY SER LEU SER PRO GLU HIS SEQRES 17 B 298 GLY PRO VAL VAL VAL HIS CYS SER ALA GLY ILE GLY ARG SEQRES 18 B 298 SER GLY THR PHE CYS LEU ALA ASP THR CYS LEU LEU LEU SEQRES 19 B 298 MET ASP LYS ARG LYS ASP PRO SER SER VAL ASP ILE LYS SEQRES 20 B 298 LYS VAL LEU LEU GLU MET ARG LYS PHE ARG MET GLY LEU SEQRES 21 B 298 ILE GLN THR ALA ASP GLN LEU ARG PHE SER TYR LEU ALA SEQRES 22 B 298 VAL ILE GLU GLY ALA LYS PHE ILE MET GLY ASP SER SER SEQRES 23 B 298 VAL GLN ASP GLN TRP LYS GLU LEU SER HIS GLU ASP HET YW9 A 301 14 HET YW9 B 301 14 HET MG B 302 1 HET CL B 303 1 HET DMS B 304 4 HETNAM YW9 4-(3,5-DIMETHYL-1H-PYRAZOL-1-YL)ANILINE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 YW9 2(C11 H13 N3) FORMUL 5 MG MG 2+ FORMUL 6 CL CL 1- FORMUL 7 DMS C2 H6 O S FORMUL 8 HOH *642(H2 O) HELIX 1 AA1 GLU A 2 GLY A 14 1 13 HELIX 2 AA2 SER A 15 ALA A 27 1 13 HELIX 3 AA3 LEU A 37 ASN A 44 5 8 HELIX 4 AA4 THR A 91 LYS A 103 1 13 HELIX 5 AA5 PRO A 188 SER A 201 1 14 HELIX 6 AA6 GLY A 220 ARG A 238 1 19 HELIX 7 AA7 ASP A 240 VAL A 244 5 5 HELIX 8 AA8 ASP A 245 ARG A 254 1 10 HELIX 9 AA9 THR A 263 MET A 282 1 20 HELIX 10 AB1 ASP A 284 GLN A 288 5 5 HELIX 11 AB2 GLU B 2 GLY B 14 1 13 HELIX 12 AB3 SER B 15 ALA B 27 1 13 HELIX 13 AB4 LEU B 37 ASN B 44 5 8 HELIX 14 AB5 THR B 91 LYS B 103 1 13 HELIX 15 AB6 PRO B 188 SER B 201 1 14 HELIX 16 AB7 GLY B 220 ARG B 238 1 19 HELIX 17 AB8 ASP B 240 VAL B 244 5 5 HELIX 18 AB9 ASP B 245 ARG B 254 1 10 HELIX 19 AC1 THR B 263 MET B 282 1 20 SHEET 1 AA1 9 ARG A 56 LYS A 58 0 SHEET 2 AA1 9 TYR A 66 MET A 74 -1 O ALA A 69 N ILE A 57 SHEET 3 AA1 9 ARG A 79 THR A 84 -1 O TYR A 81 N ILE A 72 SHEET 4 AA1 9 VAL A 211 HIS A 214 1 O VAL A 213 N ILE A 82 SHEET 5 AA1 9 GLY A 106 MET A 109 1 N VAL A 108 O VAL A 212 SHEET 6 AA1 9 THR A 168 TYR A 176 1 O PHE A 174 N VAL A 107 SHEET 7 AA1 9 TYR A 153 ASN A 162 -1 N THR A 154 O HIS A 175 SHEET 8 AA1 9 LEU A 140 ILE A 149 -1 N LYS A 141 O GLU A 161 SHEET 9 AA1 9 MET A 133 PHE A 135 -1 N PHE A 135 O LEU A 140 SHEET 1 AA2 2 MET A 114 GLU A 115 0 SHEET 2 AA2 2 SER A 118 LEU A 119 -1 O SER A 118 N GLU A 115 SHEET 1 AA3 9 ARG B 56 LYS B 58 0 SHEET 2 AA3 9 TYR B 66 MET B 74 -1 O ALA B 69 N ILE B 57 SHEET 3 AA3 9 ARG B 79 THR B 84 -1 O TYR B 81 N ILE B 72 SHEET 4 AA3 9 VAL B 211 HIS B 214 1 O VAL B 213 N ILE B 82 SHEET 5 AA3 9 GLY B 106 MET B 109 1 N VAL B 108 O VAL B 212 SHEET 6 AA3 9 THR B 168 TYR B 176 1 O PHE B 174 N VAL B 107 SHEET 7 AA3 9 TYR B 153 ASN B 162 -1 N LEU B 160 O ARG B 169 SHEET 8 AA3 9 LEU B 140 ILE B 149 -1 N LYS B 141 O GLU B 161 SHEET 9 AA3 9 MET B 133 PHE B 135 -1 N PHE B 135 O LEU B 140 LINK MG MG B 302 O HOH B 435 1555 1555 2.02 LINK MG MG B 302 O HOH B 483 1555 1555 2.10 LINK MG MG B 302 O HOH B 659 1555 1555 2.38 LINK MG MG B 302 O HOH B 673 1555 1555 2.05 LINK MG MG B 302 O HOH B 679 1555 1555 2.31 LINK MG MG B 302 O HOH B 688 1555 1555 2.04 CRYST1 89.440 89.440 165.760 90.00 90.00 90.00 P 43 21 2 16 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 0.011181 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006033 0.00000