PDB Short entry for 2WEF HEADER HYDROLASE 30-MAR-09 2WEF TITLE HUMAN 3'(2'), 5'-BISPHOSPHATE NUCLEOTIDASE 1 (BPNT1) IN COMPLEX WITH TITLE 2 AMP, PO4 AND MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 6-308; COMPND 5 SYNONYM: BISPHOSPHATE 3'-NUCLEOTIDASE 1, PAP-INOSITOL-1\,4- COMPND 6 PHOSPHATASE, BPNTASE 1, PIP; COMPND 7 EC: 3.1.3.7; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: C-TERMINAL HEXAHISTIDINE TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) R3 PRARE; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PNIC-CH2; SOURCE 8 OTHER_DETAILS: MGC KEYWDS HYDROLASE, SULFUR METABOLISM, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR M.MOCHE,P.SCHUTZ,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 L.G.DAHLGREN,A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM, AUTHOR 3 A.JOHANSSON,I.JOHANSSON,T.KARLBERG,T.KOTENYOVA,M.E.NILSSON,T.NYMAN, AUTHOR 4 C.PERSSON,J.SAGEMARK,H.SCHUELER,M.I.SIPONEN,A.G.THORSELL, AUTHOR 5 L.TRESAUGUES,S.VAN DER BERG,J.WEIGELT,M.WELIN,M.WISNIEWSKA, AUTHOR 6 P.NORDLUND,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 13-DEC-23 2WEF 1 REMARK LINK REVDAT 2 29-APR-15 2WEF 1 AUTHOR REMARK VERSN REVDAT 1 14-APR-09 2WEF 0 JRNL AUTH M.MOCHE,P.SCHUTZ,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA, JRNL AUTH 2 R.COLLINS,L.G.DAHLGREN,A.M.EDWARDS,S.FLODIN,A.FLORES, JRNL AUTH 3 S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON,I.JOHANSSON,T.KARLBERG, JRNL AUTH 4 T.KOTENYOVA,M.E.NILSSON,T.NYMAN,C.PERSSON,J.SAGEMARK, JRNL AUTH 5 H.SCHUELER,M.I.SIPONEN,A.G.THORSELL,L.TRESAUGUES, JRNL AUTH 6 S.VAN DEN BERG,J.WEIGELT,M.WELIN,M.WISNIEWSKA,P.NORDLUND JRNL TITL HUMAN 3'(2'), 5'-BISPHOSPHATE NUCLEOTIDASE 1 (BPNT1) IN JRNL TITL 2 COMPLEX WITH AMP, PO4 AND MAGNESIUM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24052 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1284 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1747 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1540 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.1860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2311 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : -0.01000 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): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.207 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2403 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1586 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3271 ; 1.906 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3906 ; 1.065 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 306 ; 6.339 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;36.615 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 411 ;13.503 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.634 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 378 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2659 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 443 ; 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): 1514 ; 1.239 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2443 ; 2.176 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 889 ; 3.429 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 828 ; 5.685 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2WEF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1290039194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 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 : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30231 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800 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 1JP4 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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+1/2,-Z+1/2 REMARK 290 4555 -X,-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 33.83200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.19700 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.83200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 50.19700 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: PQS 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 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 A2073 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2103 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 MET A 5 REMARK 465 ALA A 309 REMARK 465 HIS A 310 REMARK 465 HIS A 311 REMARK 465 HIS A 312 REMARK 465 HIS A 313 REMARK 465 HIS A 314 REMARK 465 HIS A 315 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 HOH A 2053 O HOH A 2055 1.95 REMARK 500 O HOH A 2053 O HOH A 2056 2.12 REMARK 500 OD1 ASN A 290 O HOH A 2233 2.13 REMARK 500 O HOH A 2053 O HOH A 2054 2.16 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 2028 O HOH A 2053 3545 2.13 REMARK 500 O HOH A 2053 O HOH A 2139 3655 2.13 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 243 CB CYS A 243 SG -0.099 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 ARG A 167 NE - CZ - NH2 ANGL. DEV. = -3.2 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 LYS A 40 -96.47 -97.08 REMARK 500 CYS A 42 -177.47 -172.16 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 74 OE1 REMARK 620 2 ASP A 117 OD1 90.1 REMARK 620 3 LEU A 119 O 167.9 87.4 REMARK 620 4 PO4 A 501 O3 95.0 95.8 97.0 REMARK 620 5 PO4 A 501 O4 99.8 163.3 85.6 70.2 REMARK 620 6 HOH A2038 O 86.4 104.7 82.8 159.5 89.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 74 OE2 REMARK 620 2 PO4 A 501 O1 98.8 REMARK 620 3 HOH A2033 O 89.5 163.1 REMARK 620 4 HOH A2035 O 171.0 89.6 81.6 REMARK 620 5 HOH A2064 O 86.0 105.9 89.3 94.8 REMARK 620 6 HOH A2249 O 89.5 81.4 84.0 88.7 171.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 117 OD2 REMARK 620 2 ASP A 120 OD1 96.3 REMARK 620 3 ASP A 247 OD1 92.9 86.3 REMARK 620 4 PO4 A 501 O3 88.8 100.4 172.9 REMARK 620 5 AMP A 601 O3' 173.3 87.0 93.3 84.8 REMARK 620 6 HOH A2206 O 98.4 162.1 82.8 90.1 79.6 REMARK 620 N 1 2 3 4 5 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 601 REMARK 999 REMARK 999 SEQUENCE REMARK 999 IN CONTRAST TO THE NATIVE ENZYME THE CLONED SEQUENCE REMARK 999 STARTS AT POSITION 6 WITH A THREONINE RESIDUE. THE CLONED REMARK 999 SEQUENCE ALSO CONTAIN A HEXAHISTIDINE TAIL IN THE C- REMARK 999 TERMINUS -AHHHHHH. DBREF 2WEF A 5 5 PDB 2WEF 2WEF 5 5 DBREF 2WEF A 6 308 UNP O95861 BPNT1_HUMAN 6 308 DBREF 2WEF A 309 315 PDB 2WEF 2WEF 309 315 SEQRES 1 A 311 MET THR VAL LEU MET ARG LEU VAL ALA SER ALA TYR SER SEQRES 2 A 311 ILE ALA GLN LYS ALA GLY MET ILE VAL ARG ARG VAL ILE SEQRES 3 A 311 ALA GLU GLY ASP LEU GLY ILE VAL GLU LYS THR CYS ALA SEQRES 4 A 311 THR ASP LEU GLN THR LYS ALA ASP ARG LEU ALA GLN MET SEQRES 5 A 311 SER ILE CYS SER SER LEU ALA ARG LYS PHE PRO LYS LEU SEQRES 6 A 311 THR ILE ILE GLY GLU GLU ASP LEU PRO SER GLU GLU VAL SEQRES 7 A 311 ASP GLN GLU LEU ILE GLU ASP SER GLN TRP GLU GLU ILE SEQRES 8 A 311 LEU LYS GLN PRO CYS PRO SER GLN TYR SER ALA ILE LYS SEQRES 9 A 311 GLU GLU ASP LEU VAL VAL TRP VAL ASP PRO LEU ASP GLY SEQRES 10 A 311 THR LYS GLU TYR THR GLU GLY LEU LEU ASP ASN VAL THR SEQRES 11 A 311 VAL LEU ILE GLY ILE ALA TYR GLU GLY LYS ALA ILE ALA SEQRES 12 A 311 GLY VAL ILE ASN GLN PRO TYR TYR ASN TYR GLU ALA GLY SEQRES 13 A 311 PRO ASP ALA VAL LEU GLY ARG THR ILE TRP GLY VAL LEU SEQRES 14 A 311 GLY LEU GLY ALA PHE GLY PHE GLN LEU LYS GLU VAL PRO SEQRES 15 A 311 ALA GLY LYS HIS ILE ILE THR THR THR ARG SER HIS SER SEQRES 16 A 311 ASN LYS LEU VAL THR ASP CYS VAL ALA ALA MET ASN PRO SEQRES 17 A 311 ASP ALA VAL LEU ARG VAL GLY GLY ALA GLY ASN LYS ILE SEQRES 18 A 311 ILE GLN LEU ILE GLU GLY LYS ALA SER ALA TYR VAL PHE SEQRES 19 A 311 ALA SER PRO GLY CYS LYS LYS TRP ASP THR CYS ALA PRO SEQRES 20 A 311 GLU VAL ILE LEU HIS ALA VAL GLY GLY LYS LEU THR ASP SEQRES 21 A 311 ILE HIS GLY ASN VAL LEU GLN TYR HIS LYS ASP VAL LYS SEQRES 22 A 311 HIS MET ASN SER ALA GLY VAL LEU ALA THR LEU ARG ASN SEQRES 23 A 311 TYR ASP TYR TYR ALA SER ARG VAL PRO GLU SER ILE LYS SEQRES 24 A 311 ASN ALA LEU VAL PRO ALA HIS HIS HIS HIS HIS HIS HET MG A 401 1 HET MG A 402 1 HET MG A 403 1 HET PO4 A 501 5 HET AMP A 601 23 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 MG 3(MG 2+) FORMUL 5 PO4 O4 P 3- FORMUL 6 AMP C10 H14 N5 O7 P FORMUL 7 HOH *251(H2 O) HELIX 1 1 THR A 6 GLY A 33 1 28 HELIX 2 2 THR A 48 PHE A 66 1 19 HELIX 3 3 ASP A 83 ILE A 87 5 5 HELIX 4 4 TRP A 92 LYS A 97 1 6 HELIX 5 5 PRO A 101 SER A 105 5 5 HELIX 6 6 LYS A 108 GLU A 110 5 3 HELIX 7 7 GLY A 121 GLU A 127 1 7 HELIX 8 8 LEU A 129 VAL A 133 5 5 HELIX 9 9 ASN A 200 ALA A 209 1 10 HELIX 10 10 GLY A 220 GLU A 230 1 11 HELIX 11 11 LYS A 244 VAL A 258 1 15 HELIX 12 12 ASN A 290 SER A 296 1 7 HELIX 13 13 PRO A 299 LEU A 306 1 8 SHEET 1 AA 2 VAL A 38 CYS A 42 0 SHEET 2 AA 2 ASP A 45 GLN A 47 -1 O ASP A 45 N LYS A 40 SHEET 1 AB 6 THR A 70 GLY A 73 0 SHEET 2 AB 6 LEU A 112 ASP A 120 1 O LEU A 112 N THR A 70 SHEET 3 AB 6 THR A 134 TYR A 141 -1 O THR A 134 N ASP A 120 SHEET 4 AB 6 LYS A 144 GLN A 152 -1 O LYS A 144 N TYR A 141 SHEET 5 AB 6 ARG A 167 VAL A 172 -1 O ARG A 167 N GLN A 152 SHEET 6 AB 6 GLY A 176 PHE A 178 -1 O GLY A 176 N VAL A 172 SHEET 1 AC 5 ALA A 214 ARG A 217 0 SHEET 2 AC 5 ILE A 191 THR A 194 1 O ILE A 192 N LEU A 216 SHEET 3 AC 5 ALA A 235 PHE A 238 1 O ALA A 235 N THR A 193 SHEET 4 AC 5 VAL A 284 THR A 287 -1 O VAL A 284 N PHE A 238 SHEET 5 AC 5 LYS A 261 THR A 263 -1 O LYS A 261 N THR A 287 LINK OE1 GLU A 74 MG MG A 402 1555 1555 2.05 LINK OE2 GLU A 74 MG MG A 403 1555 1555 2.02 LINK OD2 ASP A 117 MG MG A 401 1555 1555 2.09 LINK OD1 ASP A 117 MG MG A 402 1555 1555 2.06 LINK O LEU A 119 MG MG A 402 1555 1555 2.07 LINK OD1 ASP A 120 MG MG A 401 1555 1555 2.05 LINK OD1 ASP A 247 MG MG A 401 1555 1555 2.03 LINK MG MG A 401 O3 PO4 A 501 1555 1555 1.97 LINK MG MG A 401 O3' AMP A 601 1555 1555 2.30 LINK MG MG A 401 O HOH A2206 1555 1555 2.26 LINK MG MG A 402 O3 PO4 A 501 1555 1555 2.11 LINK MG MG A 402 O4 PO4 A 501 1555 1555 2.22 LINK MG MG A 402 O HOH A2038 1555 1555 2.09 LINK MG MG A 403 O1 PO4 A 501 1555 1555 2.01 LINK MG MG A 403 O HOH A2033 1555 1555 2.06 LINK MG MG A 403 O HOH A2035 1555 1555 2.06 LINK MG MG A 403 O HOH A2064 1555 1555 2.13 LINK MG MG A 403 O HOH A2249 1555 1555 2.22 SITE 1 AC1 7 ASP A 117 ASP A 120 ASP A 247 MG A 402 SITE 2 AC1 7 PO4 A 501 AMP A 601 HOH A2206 SITE 1 AC2 6 GLU A 74 ASP A 117 LEU A 119 MG A 401 SITE 2 AC2 6 PO4 A 501 HOH A2038 SITE 1 AC3 6 GLU A 74 PO4 A 501 HOH A2033 HOH A2035 SITE 2 AC3 6 HOH A2064 HOH A2249 SITE 1 AC4 17 ASP A 51 GLU A 74 ASP A 117 LEU A 119 SITE 2 AC4 17 ASP A 120 GLY A 121 THR A 122 MG A 401 SITE 3 AC4 17 MG A 402 MG A 403 AMP A 601 HOH A2035 SITE 4 AC4 17 HOH A2038 HOH A2064 HOH A2206 HOH A2248 SITE 5 AC4 17 HOH A2249 SITE 1 AC5 16 ASP A 120 THR A 195 HIS A 198 GLY A 220 SITE 2 AC5 16 LYS A 224 PHE A 238 GLY A 242 CYS A 243 SITE 3 AC5 16 ASP A 247 MG A 401 PO4 A 501 HOH A2118 SITE 4 AC5 16 HOH A2206 HOH A2249 HOH A2250 HOH A2251 CRYST1 38.980 67.664 100.394 90.00 90.00 90.00 P 2 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 0.025654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009961 0.00000