HEADER HYDROLASE 05-NOV-07 3B9G TITLE CRYSTAL STRUCTURE OF LOOP DELETION MUTANT OF TRYPANOSOMA VIVAX TITLE 2 NUCLEOSIDE HYDROLASE (3GTVNH) IN COMPLEX WITH IMMH COMPND MOL_ID: 1; COMPND 2 MOLECULE: IAG-NUCLEOSIDE HYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.2.2.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA VIVAX; SOURCE 3 ORGANISM_TAXID: 5699; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PQE-30 KEYWDS ROSSMANN FOLD, FLEXIBLE LOOP DELETION, TRANSITION STATE COMPLEX, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.VANDEMEULEBROUCKE,S.DE VOS,E.VAN HOLSBEKE,J.STEYAERT,W.VERSEES REVDAT 6 20-SEP-23 3B9G 1 REMARK REVDAT 5 05-OCT-22 3B9G 1 REMARK SEQADV HETSYN LINK REVDAT 4 23-AUG-17 3B9G 1 SOURCE REMARK REVDAT 3 24-FEB-09 3B9G 1 VERSN REVDAT 2 19-AUG-08 3B9G 1 JRNL REVDAT 1 22-APR-08 3B9G 0 JRNL AUTH A.VANDEMEULEBROUCKE,S.DE VOS,E.VAN HOLSBEKE,J.STEYAERT, JRNL AUTH 2 W.VERSEES JRNL TITL A FLEXIBLE LOOP AS A FUNCTIONAL ELEMENT IN THE CATALYTIC JRNL TITL 2 MECHANISM OF NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX. JRNL REF J.BIOL.CHEM. V. 283 22272 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18519562 JRNL DOI 10.1074/JBC.M803705200 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 106919 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : SAME SET OF REFLECTIONS AS REMARK 3 FOR PDB 1HOZ REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5566 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 432 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 632 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.59000 REMARK 3 B22 (A**2) : -0.90000 REMARK 3 B33 (A**2) : 1.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.39000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.008 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.252 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3B9G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045245. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8148 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 112485 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.60500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.270 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 1HOZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 10MM SODIUM ACETATE, REMARK 280 0.25M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K, PH 5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 37.44050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 3200 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 MET B -10 REMARK 465 ARG B -9 REMARK 465 GLY B -8 REMARK 465 SER B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER A 1 OG REMARK 470 LYS A 28 NZ REMARK 470 LYS A 81 CG CD CE NZ REMARK 470 GLU A 82 OE2 REMARK 470 LYS A 114 CD CE NZ REMARK 470 GLU A 129 CD OE1 OE2 REMARK 470 LYS A 153 CE NZ REMARK 470 ASN A 231 CG OD1 ND2 REMARK 470 LYS A 277 NZ REMARK 470 GLU A 290 CG CD OE1 OE2 REMARK 470 LYS B 81 CD CE NZ REMARK 470 GLU B 129 CG CD OE1 OE2 REMARK 470 LYS B 262 CD CE NZ REMARK 470 GLU B 290 CD OE1 OE2 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 560 O HOH A 727 1.74 REMARK 500 OE1 GLU A 228 O HOH A 797 2.16 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 CYS A 41 CA - CB - SG ANGL. DEV. = 8.2 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 ASN A 25 63.57 -100.28 REMARK 500 ALA A 39 -91.82 -105.11 REMARK 500 ASP A 40 38.98 -88.20 REMARK 500 MET A 61 14.72 -140.28 REMARK 500 ALA A 167 119.25 -161.54 REMARK 500 ASP A 190 80.90 -153.60 REMARK 500 ASP B 38 47.34 -72.30 REMARK 500 ALA B 39 -89.56 -100.32 REMARK 500 ASP B 40 31.05 -86.82 REMARK 500 ALA B 167 115.82 -160.21 REMARK 500 VAL B 168 -62.87 -100.11 REMARK 500 ASP B 190 81.88 -155.95 REMARK 500 ASN B 300 64.59 39.13 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 CA A 318 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 15 OD1 70.5 REMARK 620 3 ASP A 15 OD2 78.2 50.7 REMARK 620 4 THR A 137 O 95.6 79.6 129.4 REMARK 620 5 ASP A 251 OD2 142.5 72.3 74.7 82.5 REMARK 620 6 IMH A 501 O2' 115.7 133.4 84.1 139.5 86.8 REMARK 620 7 IMH A 501 O2' 122.9 130.5 83.4 135.7 79.1 7.8 REMARK 620 8 IMH A 501 O3' 138.9 143.9 137.0 77.3 77.5 62.2 59.5 REMARK 620 9 IMH A 501 O3' 138.6 139.9 140.3 71.9 76.5 67.6 64.8 5.4 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 318 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 10 OD1 REMARK 620 2 ASP B 15 OD1 69.3 REMARK 620 3 ASP B 15 OD2 78.5 51.5 REMARK 620 4 THR B 137 O 94.7 79.8 130.3 REMARK 620 5 ASP B 251 OD2 143.3 74.3 75.6 82.9 REMARK 620 6 IMH B 502 O3' 139.3 141.0 138.9 73.0 75.0 REMARK 620 7 IMH B 502 O3' 136.8 142.8 140.8 72.9 77.6 2.6 REMARK 620 8 IMH B 502 O2' 125.2 131.0 83.3 134.5 77.0 62.5 63.1 REMARK 620 9 IMH B 502 O2' 118.6 135.4 85.5 136.9 84.9 63.9 64.1 7.9 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMH A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMH B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HOZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERING REMARK 900 NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX REMARK 900 RELATED ID: 1HPO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERING REMARK 900 NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX WITH THE SUBSTRATE REMARK 900 ANALOGUE 3-DEAZ ADENOSINE REMARK 900 RELATED ID: 1KIC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERING REMARK 900 NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN REMARK 900 COMPLEX WITH INOSINE REMARK 900 RELATED ID: 1KIE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERING REMARK 900 NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: ASP10ALA MUTANT IN REMARK 900 COMPLEX WITH 3-DEAZA ADENOSINE REMARK 900 RELATED ID: 1R4F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN INOSINE-ADENOSINE-GUANOSINE PREFERING REMARK 900 NUCLEOSIDE HYDROLASE FROM TRYPANOSOMA VIVAX: TRP260ALA MUTANT IN REMARK 900 COMPLEX WITH 3-DEAZA ADENOSINE REMARK 900 RELATED ID: 2MAS RELATED DB: PDB REMARK 900 PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR REMARK 999 REMARK 999 DELETED LOOP C245-Y257 REPLACED BY LINKER G245-G247 DBREF 3B9G A 2 244 UNP Q9GPQ4 Q9GPQ4_TRYVI 2 244 DBREF 3B9G B 2 244 UNP Q9GPQ4 Q9GPQ4_TRYVI 2 244 DBREF 3B9G A 248 317 UNP Q9GPQ4 Q9GPQ4_TRYVI 258 327 DBREF 3B9G B 248 317 UNP Q9GPQ4 Q9GPQ4_TRYVI 258 327 SEQADV 3B9G MET A -10 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G ARG A -9 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY A -8 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G SER A -7 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -6 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -5 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -4 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -3 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -2 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS A -1 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY A 0 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G SER A 1 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY A 245 UNP Q9GPQ4 SEE REMARK 999 SEQADV 3B9G GLY A 246 UNP Q9GPQ4 SEE REMARK 999 SEQADV 3B9G GLY A 247 UNP Q9GPQ4 SEE REMARK 999 SEQADV 3B9G MET B -10 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G ARG B -9 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY B -8 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G SER B -7 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -6 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -5 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -4 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -3 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -2 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G HIS B -1 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY B 0 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G SER B 1 UNP Q9GPQ4 EXPRESSION TAG SEQADV 3B9G GLY B 245 UNP Q9GPQ4 SEE REMARK 999 SEQADV 3B9G GLY B 246 UNP Q9GPQ4 SEE REMARK 999 SEQADV 3B9G GLY B 247 UNP Q9GPQ4 SEE REMARK 999 SEQRES 1 A 328 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 A 328 LYS ASN VAL VAL LEU ASP HIS ASP GLY ASN LEU ASP ASP SEQRES 3 A 328 PHE VAL ALA MET VAL LEU LEU ALA SER ASN THR GLU LYS SEQRES 4 A 328 VAL ARG LEU ILE GLY ALA LEU CYS THR ASP ALA ASP CYS SEQRES 5 A 328 PHE VAL GLU ASN GLY PHE ASN VAL THR GLY LYS ILE MET SEQRES 6 A 328 CYS LEU MET HIS ASN ASN MET ASN LEU PRO LEU PHE PRO SEQRES 7 A 328 ILE GLY LYS SER ALA ALA THR ALA VAL ASN PRO PHE PRO SEQRES 8 A 328 LYS GLU TRP ARG CYS LEU ALA LYS ASN MET ASP ASP MET SEQRES 9 A 328 PRO ILE LEU ASN ILE PRO GLU ASN VAL GLU LEU TRP ASP SEQRES 10 A 328 LYS ILE LYS ALA GLU ASN GLU LYS TYR GLU GLY GLN GLN SEQRES 11 A 328 LEU LEU ALA ASP LEU VAL MET ASN SER GLU GLU LYS VAL SEQRES 12 A 328 THR ILE CYS VAL THR GLY PRO LEU SER ASN VAL ALA TRP SEQRES 13 A 328 CYS ILE ASP LYS TYR GLY GLU LYS PHE THR SER LYS VAL SEQRES 14 A 328 GLU GLU CYS VAL ILE MET GLY GLY ALA VAL ASP VAL ARG SEQRES 15 A 328 GLY ASN VAL PHE LEU PRO SER THR ASP GLY THR ALA GLU SEQRES 16 A 328 TRP ASN ILE TYR TRP ASP PRO ALA SER ALA LYS THR VAL SEQRES 17 A 328 PHE GLY CYS PRO GLY LEU ARG ARG ILE MET PHE SER LEU SEQRES 18 A 328 ASP SER THR ASN THR VAL PRO VAL ARG SER PRO TYR VAL SEQRES 19 A 328 GLN ARG PHE GLY GLU GLN THR ASN PHE LEU LEU SER ILE SEQRES 20 A 328 LEU VAL GLY THR MET TRP ALA MET GLY GLY GLY TYR ALA SEQRES 21 A 328 TRP ASP ALA LEU THR ALA ALA TYR VAL VAL ASP GLN LYS SEQRES 22 A 328 VAL ALA ASN VAL ASP PRO VAL PRO ILE ASP VAL VAL VAL SEQRES 23 A 328 ASP LYS GLN PRO ASN GLU GLY ALA THR VAL ARG THR ASP SEQRES 24 A 328 ALA GLU ASN TYR PRO LEU THR PHE VAL ALA ARG ASN PRO SEQRES 25 A 328 GLU ALA GLU PHE PHE LEU ASP MET LEU LEU ARG SER ALA SEQRES 26 A 328 ARG ALA CYS SEQRES 1 B 328 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER ALA SEQRES 2 B 328 LYS ASN VAL VAL LEU ASP HIS ASP GLY ASN LEU ASP ASP SEQRES 3 B 328 PHE VAL ALA MET VAL LEU LEU ALA SER ASN THR GLU LYS SEQRES 4 B 328 VAL ARG LEU ILE GLY ALA LEU CYS THR ASP ALA ASP CYS SEQRES 5 B 328 PHE VAL GLU ASN GLY PHE ASN VAL THR GLY LYS ILE MET SEQRES 6 B 328 CYS LEU MET HIS ASN ASN MET ASN LEU PRO LEU PHE PRO SEQRES 7 B 328 ILE GLY LYS SER ALA ALA THR ALA VAL ASN PRO PHE PRO SEQRES 8 B 328 LYS GLU TRP ARG CYS LEU ALA LYS ASN MET ASP ASP MET SEQRES 9 B 328 PRO ILE LEU ASN ILE PRO GLU ASN VAL GLU LEU TRP ASP SEQRES 10 B 328 LYS ILE LYS ALA GLU ASN GLU LYS TYR GLU GLY GLN GLN SEQRES 11 B 328 LEU LEU ALA ASP LEU VAL MET ASN SER GLU GLU LYS VAL SEQRES 12 B 328 THR ILE CYS VAL THR GLY PRO LEU SER ASN VAL ALA TRP SEQRES 13 B 328 CYS ILE ASP LYS TYR GLY GLU LYS PHE THR SER LYS VAL SEQRES 14 B 328 GLU GLU CYS VAL ILE MET GLY GLY ALA VAL ASP VAL ARG SEQRES 15 B 328 GLY ASN VAL PHE LEU PRO SER THR ASP GLY THR ALA GLU SEQRES 16 B 328 TRP ASN ILE TYR TRP ASP PRO ALA SER ALA LYS THR VAL SEQRES 17 B 328 PHE GLY CYS PRO GLY LEU ARG ARG ILE MET PHE SER LEU SEQRES 18 B 328 ASP SER THR ASN THR VAL PRO VAL ARG SER PRO TYR VAL SEQRES 19 B 328 GLN ARG PHE GLY GLU GLN THR ASN PHE LEU LEU SER ILE SEQRES 20 B 328 LEU VAL GLY THR MET TRP ALA MET GLY GLY GLY TYR ALA SEQRES 21 B 328 TRP ASP ALA LEU THR ALA ALA TYR VAL VAL ASP GLN LYS SEQRES 22 B 328 VAL ALA ASN VAL ASP PRO VAL PRO ILE ASP VAL VAL VAL SEQRES 23 B 328 ASP LYS GLN PRO ASN GLU GLY ALA THR VAL ARG THR ASP SEQRES 24 B 328 ALA GLU ASN TYR PRO LEU THR PHE VAL ALA ARG ASN PRO SEQRES 25 B 328 GLU ALA GLU PHE PHE LEU ASP MET LEU LEU ARG SER ALA SEQRES 26 B 328 ARG ALA CYS HET CA A 318 1 HET NA A 319 1 HET IMH A 501 38 HET CA B 318 1 HET IMH B 502 38 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM IMH 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D- HETNAM 2 IMH RIBITOL HETSYN IMH FORODESINE; IMMUCILLIN H FORMUL 3 CA 2(CA 2+) FORMUL 4 NA NA 1+ FORMUL 5 IMH 2(C11 H14 N4 O4) FORMUL 8 HOH *632(H2 O) HELIX 1 1 ASN A 12 ASN A 25 1 14 HELIX 2 2 PHE A 42 ASN A 62 1 21 HELIX 3 3 PRO A 80 CYS A 85 1 6 HELIX 4 4 CYS A 85 ASP A 92 1 8 HELIX 5 5 MET A 93 ASN A 97 5 5 HELIX 6 6 ILE A 98 LYS A 114 1 17 HELIX 7 7 GLU A 116 SER A 128 1 13 HELIX 8 8 LEU A 140 GLY A 151 1 12 HELIX 9 9 GLY A 151 SER A 156 1 6 HELIX 10 10 GLU A 184 TRP A 189 1 6 HELIX 11 11 ASP A 190 GLY A 199 1 10 HELIX 12 12 SER A 209 ASN A 214 1 6 HELIX 13 13 ARG A 219 PHE A 226 1 8 HELIX 14 14 GLY A 227 THR A 230 5 4 HELIX 15 15 PHE A 232 GLY A 245 1 14 HELIX 16 16 ALA A 249 ASP A 260 1 12 HELIX 17 17 GLN A 261 ALA A 264 5 4 HELIX 18 18 GLU A 302 ALA A 314 1 13 HELIX 19 19 ASN B 12 ASN B 25 1 14 HELIX 20 20 PHE B 42 ASN B 59 1 18 HELIX 21 21 PRO B 80 CYS B 85 1 6 HELIX 22 22 CYS B 85 ASP B 92 1 8 HELIX 23 23 MET B 93 ASN B 97 5 5 HELIX 24 24 ILE B 98 LYS B 114 1 17 HELIX 25 25 GLU B 116 SER B 128 1 13 HELIX 26 26 LEU B 140 GLY B 151 1 12 HELIX 27 27 GLY B 151 SER B 156 1 6 HELIX 28 28 GLU B 184 TRP B 189 1 6 HELIX 29 29 ASP B 190 GLY B 199 1 10 HELIX 30 30 SER B 209 ASN B 214 1 6 HELIX 31 31 ARG B 219 ARG B 225 1 7 HELIX 32 32 PHE B 226 THR B 230 5 5 HELIX 33 33 PHE B 232 GLY B 245 1 14 HELIX 34 34 ALA B 249 ASP B 260 1 12 HELIX 35 35 GLN B 261 ALA B 264 5 4 HELIX 36 36 GLU B 302 ALA B 314 1 13 SHEET 1 A 9 ILE A 68 LYS A 70 0 SHEET 2 A 9 VAL A 29 CYS A 36 1 N CYS A 36 O GLY A 69 SHEET 3 A 9 LYS A 3 HIS A 9 1 N LYS A 3 O ARG A 30 SHEET 4 A 9 VAL A 132 VAL A 136 1 O CYS A 135 N ASP A 8 SHEET 5 A 9 VAL A 158 MET A 164 1 O MET A 164 N VAL A 136 SHEET 6 A 9 ARG A 205 PHE A 208 1 O PHE A 208 N ILE A 163 SHEET 7 A 9 LEU A 294 ARG A 299 1 O ALA A 298 N MET A 207 SHEET 8 A 9 ASN A 265 VAL A 273 -1 N ASP A 267 O VAL A 297 SHEET 9 A 9 THR A 284 ARG A 286 -1 O VAL A 285 N ASP A 272 SHEET 1 B 9 ILE B 68 LYS B 70 0 SHEET 2 B 9 VAL B 29 CYS B 36 1 N ALA B 34 O GLY B 69 SHEET 3 B 9 LYS B 3 HIS B 9 1 N LYS B 3 O ARG B 30 SHEET 4 B 9 VAL B 132 VAL B 136 1 O CYS B 135 N ASP B 8 SHEET 5 B 9 VAL B 158 MET B 164 1 O VAL B 162 N ILE B 134 SHEET 6 B 9 ARG B 205 PHE B 208 1 O PHE B 208 N ILE B 163 SHEET 7 B 9 LEU B 294 ARG B 299 1 O ALA B 298 N MET B 207 SHEET 8 B 9 ASN B 265 VAL B 273 -1 N ASP B 267 O VAL B 297 SHEET 9 B 9 THR B 284 ARG B 286 -1 O VAL B 285 N ASP B 272 LINK OD1 ASP A 10 CA CA A 318 1555 1555 2.48 LINK OD1 ASP A 15 CA CA A 318 1555 1555 2.57 LINK OD2 ASP A 15 CA CA A 318 1555 1555 2.48 LINK OE2 GLU A 44 NA NA A 319 1555 1555 2.13 LINK O THR A 137 CA CA A 318 1555 1555 2.39 LINK OD2 ASP A 251 CA CA A 318 1555 1555 2.44 LINK CA CA A 318 O2'AIMH A 501 1555 1555 2.65 LINK CA CA A 318 O2'BIMH A 501 1555 1555 2.33 LINK CA CA A 318 O3'AIMH A 501 1555 1555 2.36 LINK CA CA A 318 O3'BIMH A 501 1555 1555 2.56 LINK CA CA A 318 O HOH A 514 1555 1555 2.43 LINK OD1 ASP B 10 CA CA B 318 1555 1555 2.46 LINK OD1 ASP B 15 CA CA B 318 1555 1555 2.58 LINK OD2 ASP B 15 CA CA B 318 1555 1555 2.47 LINK O THR B 137 CA CA B 318 1555 1555 2.36 LINK OD2 ASP B 251 CA CA B 318 1555 1555 2.42 LINK CA CA B 318 O3'AIMH B 502 1555 1555 2.52 LINK CA CA B 318 O3'BIMH B 502 1555 1555 2.54 LINK CA CA B 318 O2'BIMH B 502 1555 1555 2.40 LINK CA CA B 318 O2'AIMH B 502 1555 1555 2.49 LINK CA CA B 318 O HOH B 523 1555 1555 2.47 SITE 1 AC1 5 ASP A 10 ASP A 15 THR A 137 ASP A 251 SITE 2 AC1 5 HOH A 514 SITE 1 AC2 5 ASP B 10 ASP B 15 THR B 137 ASP B 251 SITE 2 AC2 5 HOH B 523 SITE 1 AC3 3 GLU A 44 LYS A 70 GLU A 113 SITE 1 AC4 16 ASN A 12 ASP A 14 ASP A 15 ASP A 40 SITE 2 AC4 16 TRP A 83 THR A 137 MET A 164 ASN A 173 SITE 3 AC4 16 GLU A 184 TRP A 185 ASN A 186 TRP A 250 SITE 4 AC4 16 ASP A 251 HOH A 514 HOH A 611 HOH A 783 SITE 1 AC5 17 ASN B 12 ASP B 14 ASP B 15 ASP B 40 SITE 2 AC5 17 TRP B 83 THR B 137 MET B 164 ASN B 173 SITE 3 AC5 17 GLU B 184 TRP B 185 ASN B 186 TRP B 250 SITE 4 AC5 17 ASP B 251 HOH B 523 HOH B 646 HOH B 767 SITE 5 AC5 17 HOH B 768 CRYST1 54.177 74.881 72.424 90.00 98.07 90.00 P 1 21 1 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 0.018458 0.000000 0.002617 0.00000 SCALE2 0.000000 0.013355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013946 0.00000