HEADER HYDROLASE/HYDROLASE INHIBITOR 30-NOV-12 4I71 TITLE CRYSTAL STRUCTURE OF THE TRYPANOSOMA BRUCEI INOSINE-ADENOSINE- TITLE 2 GUANOSINE NUCLEOSIDE HYDROLASE IN COMPLEX WITH A TRYPANOCIDAL TITLE 3 COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: INOSINE-ADENOSINE-GUANOSINE-NUCLEOSIDE HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.2.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 999953; SOURCE 4 STRAIN: 927/4 GUTAT10.1; SOURCE 5 GENE: TB927.3.2960; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS NUCLEOSIDE HYDROLASE, OPEN (ALPHA, BETA) STRUCTURE, NH FOLD, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.GIANNESE,M.DEGANO REVDAT 3 08-NOV-23 4I71 1 REMARK SEQADV LINK REVDAT 2 18-DEC-13 4I71 1 JRNL REVDAT 1 07-AUG-13 4I71 0 JRNL AUTH F.GIANNESE,M.BERG,P.VAN DER VEKEN,V.CASTAGNA,P.TORNAGHI, JRNL AUTH 2 K.AUGUSTYNS,M.DEGANO JRNL TITL STRUCTURES OF PURINE NUCLEOSIDASE FROM TRYPANOSOMA BRUCEI JRNL TITL 2 BOUND TO ISOZYME-SPECIFIC TRYPANOCIDALS AND A NOVEL JRNL TITL 3 METALORGANIC INHIBITOR JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 1553 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23897478 JRNL DOI 10.1107/S0907444913010792 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.VERSEES,J.BARLOW,J.STEYAERT REMARK 1 TITL TRANSITION-STATE COMPLEX OF THE PURINE-SPECIFIC NUCLEOSIDE REMARK 1 TITL 2 HYDROLASE OF T. VIVAX: ENZYME CONFORMATIONAL CHANGES AND REMARK 1 TITL 3 IMPLICATIONS FOR CATALYSIS REMARK 1 REF J.MOL.BIOL. V. 359 331 2006 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 16630632 REMARK 1 DOI 10.1016/J.JMB.2006.03.026 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.VANDEMEULEBROUCKE,C.MINICI,I.BRUNO,L.MUZZOLINI,P.TORNAGHI, REMARK 1 AUTH 2 D.W.PARKIN,W.VERSEES,J.STEYAERT,M.DEGANO REMARK 1 TITL STRUCTURE AND MECHANISM OF THE 6-OXOPURINE NUCLEOSIDASE FROM REMARK 1 TITL 2 TRYPANOSOMA BRUCEI BRUCEI REMARK 1 REF BIOCHEMISTRY V. 49 8999 2010 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 20825170 REMARK 1 DOI 10.1021/BI100697D REMARK 1 REFERENCE 3 REMARK 1 AUTH D.W.PARKIN REMARK 1 TITL PURINE-SPECIFIC NUCLEOSIDE N-RIBOHYDROLASE FROM TRYPANOSOMA REMARK 1 TITL 2 BRUCEI BRUCEI. PURIFICATION, SPECIFICITY, AND KINETIC REMARK 1 TITL 3 MECHANISM REMARK 1 REF J.BIOL.CHEM. V. 271 21713 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 8702965 REMARK 2 REMARK 2 RESOLUTION. 1.28 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) : 1.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 133.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 78467 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) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3944 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) : 1.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3303 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 57.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.1770 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.2100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 282 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.04000 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): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.020 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.990 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2646 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1767 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3607 ; 1.744 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4351 ; 1.037 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 6.177 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 105 ;36.482 ;24.952 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 450 ;12.971 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;10.523 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 411 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2911 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 500 ; 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): 1659 ; 2.308 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 662 ; 1.486 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2693 ; 3.106 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 987 ; 4.023 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 908 ; 5.497 ; 5.500 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): 4413 ; 1.990 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 287 ;11.817 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4349 ; 4.949 ; 3.000 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 : 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: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4I71 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076384. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : SILICON CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78467 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.280 REMARK 200 RESOLUTION RANGE LOW (A) : 133.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 57.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.840 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: 1KIC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 19% PEGMME2000, 10MM REMARK 280 NI2SO4, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.64000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.64000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 33.18000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.17500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.18000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.17500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.64000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.18000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.17500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.64000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.18000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.17500 REMARK 290 SMTRY3 8 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: 3080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.64000 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 298 REMARK 465 GLY A 299 REMARK 465 GLU A 300 REMARK 465 GLY A 301 REMARK 465 LYS A 302 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 GLU A 82 CD GLU A 82 OE1 0.080 REMARK 500 TRP A 242 CG TRP A 242 CD1 0.093 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 293 NE - CZ - NH2 ANGL. DEV. = -3.1 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 SER A -1 -12.47 169.23 REMARK 500 ALA A 39 -90.76 -105.33 REMARK 500 ASP A 40 31.59 -85.38 REMARK 500 VAL A 168 -60.27 -97.79 REMARK 500 ASP A 190 82.49 -153.76 REMARK 500 THR A 294 67.71 -118.93 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 NI A 404 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -2 N REMARK 620 2 SER A -1 N 83.9 REMARK 620 3 HIS A 0 ND1 97.9 174.9 REMARK 620 4 HIS A 0 N 166.5 82.8 95.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 15 OD2 80.6 REMARK 620 3 ASP A 15 OD1 73.5 52.6 REMARK 620 4 THR A 137 O 93.0 135.4 83.1 REMARK 620 5 ASP A 261 OD2 145.4 76.1 72.0 86.0 REMARK 620 6 AGV A 401 O2' 131.2 75.8 119.7 133.0 66.6 REMARK 620 7 AGV A 401 O3' 138.4 136.9 139.0 72.2 74.0 64.1 REMARK 620 8 HOH A 504 O 72.1 122.5 145.4 96.4 142.5 85.7 71.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 403 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 58 NE2 REMARK 620 2 TRS A 405 O1 92.3 REMARK 620 3 TRS A 405 N 172.2 85.3 REMARK 620 4 TRS A 405 O2 91.7 85.2 80.7 REMARK 620 5 TRS A 405 O3 158.8 83.0 28.1 108.3 REMARK 620 6 TRS A 405 O1 91.7 0.8 86.0 85.8 83.3 REMARK 620 7 TRS A 405 O2 94.7 67.8 77.5 17.6 102.4 68.4 REMARK 620 8 HOH A 501 O 91.2 173.1 90.4 88.8 95.8 173.9 106.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 407 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 317 NE2 REMARK 620 2 HOH A 656 O 94.4 REMARK 620 3 HOH A 701 O 105.9 149.8 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 AGV A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EPW RELATED DB: PDB REMARK 900 T.VIVAX IAGNH BOUND TO A N-METHYLARYL IMINORIBITOL INHIBITOR REMARK 900 RELATED ID: 3FZ0 RELATED DB: PDB REMARK 900 T. BRUCEI IGNH REMARK 900 RELATED ID: 4I70 RELATED DB: PDB REMARK 900 RELATED ID: 4I72 RELATED DB: PDB REMARK 900 RELATED ID: 4I73 RELATED DB: PDB REMARK 900 RELATED ID: 4I74 RELATED DB: PDB REMARK 900 RELATED ID: 4I75 RELATED DB: PDB DBREF 4I71 A 1 327 UNP Q57ZL6 Q57ZL6_TRYB2 1 327 SEQADV 4I71 GLY A -2 UNP Q57ZL6 EXPRESSION TAG SEQADV 4I71 SER A -1 UNP Q57ZL6 EXPRESSION TAG SEQADV 4I71 HIS A 0 UNP Q57ZL6 EXPRESSION TAG SEQRES 1 A 330 GLY SER HIS MET ALA LYS THR VAL ILE LEU ASP HIS ASP SEQRES 2 A 330 GLY ASN LYS ASP ASP PHE VAL ALA MET ILE LEU LEU LEU SEQRES 3 A 330 SER ASN PRO LYS LYS VAL ASN LEU ILE GLY CYS ILE CYS SEQRES 4 A 330 THR ASP ALA ASP CYS PHE VAL GLU ASN GLY PHE ASP VAL SEQRES 5 A 330 THR GLY LYS ILE MET CYS ALA MET HIS ARG LEU ILE LYS SEQRES 6 A 330 THR PRO LEU PHE PRO ILE GLY LYS SER THR ALA THR ALA SEQRES 7 A 330 VAL ASN ALA PHE PRO THR GLU TRP ARG PHE SER ALA LYS SEQRES 8 A 330 ASN LEU ASP ASP MET PRO PHE LEU ASN ILE VAL GLU ASP SEQRES 9 A 330 VAL ALA LEU TRP GLU LYS LEU LYS PRO GLU ASN GLU ALA SEQRES 10 A 330 HIS ASN GLY GLN GLN LEU LEU ALA ASP LEU VAL MET LYS SEQRES 11 A 330 SER LYS GLU LYS VAL THR VAL CYS VAL THR GLY PRO LEU SEQRES 12 A 330 SER ASN MET ALA TRP CYS ILE GLU LYS TYR GLY GLU ALA SEQRES 13 A 330 PHE THR SER LYS VAL GLU GLU CYS VAL ILE MET GLY GLY SEQRES 14 A 330 ALA VAL ASP VAL GLY GLY ASN VAL PHE LEU PRO THR THR SEQRES 15 A 330 ASP GLY SER ALA GLU TRP ASN ILE TYR TRP ASP PRO PRO SEQRES 16 A 330 ALA ALA LYS LYS VAL LEU CYS CYS PRO ASN ILE ARG CYS SEQRES 17 A 330 VAL LEU PHE SER LEU ASP ALA THR ASN THR VAL PRO VAL SEQRES 18 A 330 ARG SER VAL ASP VAL LYS GLY PHE GLY ALA GLN ASN GLN SEQRES 19 A 330 TYR LEU LEU SER GLN MET VAL GLY THR MET TRP ALA MET SEQRES 20 A 330 SER THR HIS GLU GLU ILE LEU ARG ASP GLY ASP ALA TYR SEQRES 21 A 330 TYR ALA TRP ASP ALA LEU THR ALA ALA TYR ILE LEU GLU SEQRES 22 A 330 PRO THR ILE ALA THR LEU GLU PRO VAL ALA LEU ASP VAL SEQRES 23 A 330 ASP VAL SER LYS GLY LYS SER GLU GLY ARG THR PRO ARG SEQRES 24 A 330 ALA SER GLY GLU GLY LYS PRO CYS VAL HIS VAL ALA ARG SEQRES 25 A 330 ASN PRO SER LYS GLN MET PHE HIS ASP LEU VAL PHE ALA SEQRES 26 A 330 SER THR ARG VAL CYS HET AGV A 401 20 HET CA A 402 1 HET NI A 403 1 HET NI A 404 1 HET TRS A 405 16 HET NI A 406 1 HET NI A 407 1 HETNAM AGV (2R,3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7- HETNAM 2 AGV YL)METHYL]-2-(HYDROXYMETHYL)PYRROLIDINE-3,4-DIOL HETNAM CA CALCIUM ION HETNAM NI NICKEL (II) ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 AGV C12 H17 N5 O3 FORMUL 3 CA CA 2+ FORMUL 4 NI 4(NI 2+) FORMUL 6 TRS C4 H12 N O3 1+ FORMUL 9 HOH *282(H2 O) HELIX 1 1 ASN A 12 SER A 24 1 13 HELIX 2 2 PHE A 42 LYS A 62 1 21 HELIX 3 3 PRO A 80 PHE A 85 1 6 HELIX 4 4 PHE A 85 ASP A 92 1 8 HELIX 5 5 MET A 93 ASN A 97 5 5 HELIX 6 6 ILE A 98 ALA A 114 1 17 HELIX 7 7 ASN 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 ASP A 190 1 7 HELIX 11 11 ASP A 190 CYS A 199 1 10 HELIX 12 12 SER A 209 ASN A 214 1 6 HELIX 13 13 ARG A 219 LYS A 224 1 6 HELIX 14 14 GLY A 225 ASN A 230 5 6 HELIX 15 15 TYR A 232 MET A 244 1 13 HELIX 16 16 HIS A 247 ARG A 252 1 6 HELIX 17 17 ALA A 259 GLU A 270 1 12 HELIX 18 18 PRO A 271 ALA A 274 5 4 HELIX 19 19 SER A 312 THR A 324 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 ASN 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 CYS A 205 PHE A 208 1 O PHE A 208 N ILE A 163 SHEET 7 A 9 CYS A 304 ARG A 309 1 O ALA A 308 N LEU A 207 SHEET 8 A 9 THR A 275 LEU A 281 -1 N THR A 275 O ARG A 309 SHEET 9 A 9 ARG A 296 ALA A 297 -1 O ALA A 297 N ALA A 280 SSBOND 1 CYS A 199 CYS A 304 1555 1555 2.07 LINK N GLY A -2 NI NI A 404 1555 1555 1.97 LINK N SER A -1 NI NI A 404 1555 1555 1.99 LINK ND1 HIS A 0 NI NI A 404 1555 1555 1.87 LINK N HIS A 0 NI NI A 404 1555 1555 1.99 LINK OD1 ASP A 10 CA CA A 402 1555 1555 2.35 LINK OD2 ASP A 15 CA CA A 402 1555 1555 2.47 LINK OD1 ASP A 15 CA CA A 402 1555 1555 2.54 LINK NE2 HIS A 58 NI NI A 403 1555 1555 2.05 LINK NE2 HIS A 115 NI NI A 406 1555 1555 2.05 LINK O THR A 137 CA CA A 402 1555 1555 2.32 LINK OD2 ASP A 261 CA CA A 402 1555 1555 2.50 LINK NE2 HIS A 317 NI NI A 407 1555 1555 2.05 LINK O2' AGV A 401 CA CA A 402 1555 1555 2.43 LINK O3' AGV A 401 CA CA A 402 1555 1555 2.55 LINK CA CA A 402 O HOH A 504 1555 1555 2.53 LINK NI NI A 403 O1 ATRS A 405 1555 1555 1.99 LINK NI NI A 403 N ATRS A 405 1555 1555 2.08 LINK NI NI A 403 O2 ATRS A 405 1555 1555 2.08 LINK NI NI A 403 O3 BTRS A 405 1555 1555 2.26 LINK NI NI A 403 O1 BTRS A 405 1555 1555 2.29 LINK NI NI A 403 O2 BTRS A 405 1555 1555 2.36 LINK NI NI A 403 O HOH A 501 1555 1555 2.06 LINK NI NI A 407 O HOH A 656 1555 1555 2.22 LINK NI NI A 407 O HOH A 701 1555 1555 2.17 SITE 1 AC1 19 ASN A 12 ASP A 14 ASP A 15 ASP A 40 SITE 2 AC1 19 PHE A 79 TRP A 83 THR A 137 ASN A 173 SITE 3 AC1 19 GLU A 184 ASN A 186 GLU A 248 ARG A 252 SITE 4 AC1 19 TYR A 257 TRP A 260 ASP A 261 CA A 402 SITE 5 AC1 19 HOH A 504 HOH A 535 HOH A 559 SITE 1 AC2 6 ASP A 10 ASP A 15 THR A 137 ASP A 261 SITE 2 AC2 6 AGV A 401 HOH A 504 SITE 1 AC3 4 HIS A 58 ASP A 253 TRS A 405 HOH A 501 SITE 1 AC4 3 GLY A -2 SER A -1 HIS A 0 SITE 1 AC5 12 HIS A 58 LEU A 65 LEU A 104 LYS A 107 SITE 2 AC5 12 ILE A 250 LEU A 251 ASP A 253 NI A 403 SITE 3 AC5 12 HOH A 501 HOH A 586 HOH A 687 HOH A 773 SITE 1 AC6 1 HIS A 115 SITE 1 AC7 3 HIS A 317 HOH A 656 HOH A 701 CRYST1 66.360 72.350 133.280 90.00 90.00 90.00 C 2 2 21 8 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 0.015069 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007503 0.00000