HEADER HYDROLASE 13-JUN-00 1F5D OBSLTE 19-DEC-01 1F5D 1J4X TITLE HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE C124S MUTANT- TITLE 2 PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUAL SPECIFICITY PROTEIN PHOSPHATASE 3; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.3.48; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN (11-MER); COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7-VHR; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS HYDROLASE, PROTEIN DUAL-SPECIFICITY PHOSPHATASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SCHUMACHER,J.L.TODD,K.G.TANNER,J.M.DENU REVDAT 3 19-DEC-01 1F5D 1 OBSLTE REVDAT 2 16-MAY-01 1F5D 1 OBSLTE REVDAT 1 13-DEC-00 1F5D 0 JRNL AUTH M.A.SCHUMACHER,J.M.DENU,K.G.TANNER,J.L.TODD JRNL TITL THE STRUCTURAL BASIS FOR RECOGNITION OF JRNL TITL 2 BISPHOSPHOR SUBSTRATES BY VHR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 9236 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD :NULL REMARK 3 FREE R VALUE TEST SET SELECTION :RANDOM REMARK 3 R VALUE (WORKING + TEST SET) :0.192 REMARK 3 R VALUE (WORKING SET) :0.188 REMARK 3 FREE R VALUE :0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) :8.960 REMARK 3 FREE R VALUE TEST SET COUNT :810 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1920 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 16753 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 45.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.780 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F5D COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-JUN-2000. REMARK 100 THE RCSB ID CODE IS RCSB011262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-1997 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : 7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9234 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: MERLOT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ISOPROPANOL, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-Z 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 17.19500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.56500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.56500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.19500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, D 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 SER A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 PHE A 5 REMARK 465 GLU A 6 REMARK 465 LEU A 7 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 REMARK 500 O LEU A 98 O HOH 252 2.15 REMARK 500 N PHE A 102 O HOH 252 2.16 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 36 CB ARG A 36 CG 4.021 REMARK 500 ARG A 36 CG ARG A 36 CD 2.026 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 36 CA - CB - CG ANGL. DEV. =-32.9 DEGREES REMARK 500 ARG A 36 CB - CG - CD ANGL. DEV. =-82.4 DEGREES REMARK 500 ARG A 36 CG - CD - NE ANGL. DEV. = 32.9 DEGREES REMARK 500 VAL D 11 N - CA - C ANGL. DEV. = 25.4 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 TPO D 8 -54.14 39.84 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 200 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH 204 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH 205 DISTANCE = 5.20 ANGSTROMS REMARK 525 HOH 211 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH 215 DISTANCE = 5.68 ANGSTROMS REMARK 525 HOH 223 DISTANCE = 11.14 ANGSTROMS REMARK 525 HOH 226 DISTANCE = 8.94 ANGSTROMS REMARK 525 HOH 227 DISTANCE = 7.12 ANGSTROMS REMARK 525 HOH 228 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH 237 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH 238 DISTANCE = 6.59 ANGSTROMS REMARK 525 HOH 239 DISTANCE = 8.46 ANGSTROMS REMARK 525 HOH 243 DISTANCE = 8.90 ANGSTROMS REMARK 525 HOH 245 DISTANCE = 7.28 ANGSTROMS REMARK 525 HOH 255 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH 258 DISTANCE = 17.35 ANGSTROMS REMARK 525 HOH 264 DISTANCE = 10.27 ANGSTROMS DBREF 1F5D A 2 185 UNP P51452 DUS3_HUMAN 2 185 SEQADV 1F5D SER A 124 UNP P51452 CYS 124 ENGINEERED SEQRES 1 A 184 SER GLY SER PHE GLU LEU SER VAL GLN ASP LEU ASN ASP SEQRES 2 A 184 LEU LEU SER ASP GLY SER GLY CYS TYR SER LEU PRO SER SEQRES 3 A 184 GLN PRO CYS ASN GLU VAL THR PRO ARG ILE TYR VAL GLY SEQRES 4 A 184 ASN ALA SER VAL ALA GLN ASP ILE PRO LYS LEU GLN LYS SEQRES 5 A 184 LEU GLY ILE THR HIS VAL LEU ASN ALA ALA GLU GLY ARG SEQRES 6 A 184 SER PHE MET HIS VAL ASN THR ASN ALA ASN PHE TYR LYS SEQRES 7 A 184 ASP SER GLY ILE THR TYR LEU GLY ILE LYS ALA ASN ASP SEQRES 8 A 184 THR GLN GLU PHE ASN LEU SER ALA TYR PHE GLU ARG ALA SEQRES 9 A 184 ALA ASP PHE ILE ASP GLN ALA LEU ALA GLN LYS ASN GLY SEQRES 10 A 184 ARG VAL LEU VAL HIS SER ARG GLU GLY TYR SER ARG SER SEQRES 11 A 184 PRO THR LEU VAL ILE ALA TYR LEU MET MET ARG GLN LYS SEQRES 12 A 184 MET ASP VAL LYS SER ALA LEU SER ILE VAL ARG GLN ASN SEQRES 13 A 184 ARG GLU ILE GLY PRO ASN ASP GLY PHE LEU ALA GLN LEU SEQRES 14 A 184 CYS GLN LEU ASN ASP ARG LEU ALA LYS GLU GLY LYS LEU SEQRES 15 A 184 LYS PRO SEQRES 1 D 11 ASP ASP GLU AHP TPO GLY PTR VAL ALA THR ARG MODRES 1F5D AHP D 7 ALA 2-AMINO-HEPTANOIC ACID MODRES 1F5D TPO D 8 THR PHOSPHOTHREONINE MODRES 1F5D PTR D 10 TYR PHOSPHOTYROSINE HET AHP D 7 9 HET TPO D 8 11 HET PTR D 10 16 HETNAM AHP 2-AMINO-HEPTANOIC ACID HETNAM TPO PHOSPHOTHREONINE HETNAM PTR O-PHOSPHOTYROSINE HETSYN TPO PHOSPHONOTHREONINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 2 AHP C7 H15 N O2 FORMUL 2 TPO C4 H10 N O6 P FORMUL 2 PTR C9 H12 N O6 P FORMUL 3 HOH *66(H2 O1) HELIX 1 1 SER A 8 SER A 17 1 10 HELIX 2 2 ASN A 41 GLN A 46 1 6 HELIX 3 3 ASP A 47 LEU A 54 1 8 HELIX 4 4 ASN A 74 LYS A 79 1 6 HELIX 5 5 ASN A 97 ALA A 100 5 4 HELIX 6 6 TYR A 101 GLN A 115 1 15 HELIX 7 7 SER A 129 GLN A 143 1 15 HELIX 8 8 ASP A 146 ARG A 158 1 13 HELIX 9 9 ASN A 163 GLU A 180 1 18 SHEET 1 A 5 CYS A 30 THR A 34 0 SHEET 2 A 5 ILE A 37 GLY A 40 -1 N ILE A 37 O THR A 34 SHEET 3 A 5 VAL A 120 HIS A 123 1 O VAL A 120 N TYR A 38 SHEET 4 A 5 HIS A 58 ASN A 61 1 O HIS A 58 N LEU A 121 SHEET 5 A 5 THR A 84 GLY A 87 1 O THR A 84 N VAL A 59 CISPEP 1 GLY D 9 PTR D 10 0 0.33 CRYST1 34.390 55.770 101.130 90.00 90.00 90.00 P 21 21 21 4 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 0.029078 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017931 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009888 0.00000