HEADER HYDROLASE/HYDROLASE INHIBITOR 30-NOV-12 4I74 TITLE CRYSTAL STRUCTURE OF THE TRYPANOSOMA BRUCEI INOSINE-ADENOSINE- TITLE 2 GUANOSINE NUCLEOSIDE HYDROLASE IN COMPLEX WITH COMPOUND UAMC-00312 TITLE 3 AND ALLOSTERICALLY INHIBITED BY A NI2+ ION 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 2 18-DEC-13 4I74 1 JRNL REVDAT 1 07-AUG-13 4I74 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. 1.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.91 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31439 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1590 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) : 1.68 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2166 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2506 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 281 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : 0.63000 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): 0.102 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.100 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.905 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.954 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2655 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1754 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3625 ; 1.680 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4331 ; 1.002 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 5.236 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;35.694 ;25.189 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;12.352 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;14.250 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2942 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 499 ; 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): 1670 ; 0.887 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 669 ; 0.258 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2712 ; 1.561 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 985 ; 2.475 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 905 ; 4.124 ; 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 : 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 4I74 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 RCSB ID CODE IS RCSB076387. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND (001) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 42.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.65700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 23% PEGMME2000, 10MM REMARK 280 NI2SO4, PH 7.6, 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 65.11500 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 65.11500 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 30.06000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.71000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.06000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.71000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 65.11500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.06000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.71000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 65.11500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.06000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.71000 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: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.0 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 -60.12000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -65.11500 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 GLU A 300 REMARK 465 GLY A 301 REMARK 465 LYS A 302 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 NI NI A 402 O HOH A 764 1.14 REMARK 500 NI NI A 402 O HOH A 696 1.52 REMARK 500 O HOH A 751 O HOH A 764 1.90 REMARK 500 O HOH A 730 O HOH A 752 1.95 REMARK 500 O HOH A 737 O HOH A 766 1.98 REMARK 500 OE2 GLU A 277 O HOH A 621 2.03 REMARK 500 O HOH A 518 O HOH A 721 2.04 REMARK 500 O HOH A 705 O HOH A 757 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 NI NI A 403 O HOH A 737 5555 1.11 REMARK 500 O HOH A 733 O HOH A 734 7444 1.57 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 -4.36 -160.02 REMARK 500 ASP A 38 48.91 -76.02 REMARK 500 ALA A 39 -92.40 -103.35 REMARK 500 VAL A 168 -63.47 -96.31 REMARK 500 ASP A 190 82.02 -155.50 REMARK 500 HIS A 247 -128.43 49.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 MBY 408 AND NI 406, TRS 409 PLACE THE ALTERNATE POSITIONS. 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 406 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRS A 409 O1 REMARK 620 2 HOH A 742 O 88.3 REMARK 620 3 TRS A 409 N 89.2 168.2 REMARK 620 4 ASP A 14 OD2 102.6 93.1 98.7 REMARK 620 5 TRS A 409 O3 74.6 86.1 82.2 177.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 661 O REMARK 620 2 HOH A 751 O 176.6 REMARK 620 3 HIS A 58 NE2 88.0 90.0 REMARK 620 4 HOH A 704 O 86.9 94.9 172.7 REMARK 620 N 1 2 3 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 HOH A 725 O REMARK 620 2 HOH A 772 O 102.4 REMARK 620 3 HIS A 317 NE2 113.1 93.7 REMARK 620 N 1 2 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 HOH A 729 O REMARK 620 2 HOH A 728 O 111.6 REMARK 620 3 ASP A 190 OD2 87.8 84.4 REMARK 620 4 HOH A 780 O 78.7 169.2 100.0 REMARK 620 5 HOH A 755 O 99.1 85.3 169.2 89.6 REMARK 620 6 HOH A 540 O 155.4 92.8 98.4 76.8 78.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 405 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A -1 N REMARK 620 2 HIS A 0 ND1 168.1 REMARK 620 3 HIS A 0 N 88.1 93.0 REMARK 620 4 GLY A -2 N 79.6 99.4 167.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 410 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 757 O REMARK 620 2 HIS A 247 NE2 90.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 137 O REMARK 620 2 ASP A 10 OD1 94.4 REMARK 620 3 HOH A 742 O 149.9 98.3 REMARK 620 4 ASP A 261 OD2 85.9 146.8 97.7 REMARK 620 5 ASP A 15 OD2 135.2 78.6 74.3 78.0 REMARK 620 6 MBY A 408 O2' 132.7 127.7 29.5 70.5 80.3 REMARK 620 7 ASP A 15 OD1 83.6 74.8 126.0 72.2 51.8 123.8 REMARK 620 8 HOH A 527 O 92.3 71.7 66.5 141.6 125.6 83.3 145.8 REMARK 620 9 MBY A 408 O3' 73.5 140.0 79.3 71.8 136.4 60.5 138.3 70.9 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI 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 NI 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 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MBY A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 410 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: 4I71 RELATED DB: PDB REMARK 900 RELATED ID: 4I72 RELATED DB: PDB REMARK 900 RELATED ID: 4I73 RELATED DB: PDB REMARK 900 RELATED ID: 4I75 RELATED DB: PDB DBREF 4I74 A 1 327 UNP Q57ZL6 Q57ZL6_TRYB2 1 327 SEQADV 4I74 GLY A -2 UNP Q57ZL6 EXPRESSION TAG SEQADV 4I74 SER A -1 UNP Q57ZL6 EXPRESSION TAG SEQADV 4I74 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 CA A 401 1 HET NI A 402 1 HET NI A 403 1 HET NI A 404 1 HET NI A 405 1 HET NI A 406 1 HET NI A 407 1 HET MBY A 408 20 HET TRS A 409 8 HET NI A 410 2 HETNAM CA CALCIUM ION HETNAM NI NICKEL (II) ION HETNAM MBY (2R,3R,4S)-2-(HYDROXYMETHYL)-1-[(4-HYDROXYTHIENO[3,2- HETNAM 2 MBY D]PYRIMIDIN-7-YL)METHYL]PYRROLIDINE-3,4-DIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 CA CA 2+ FORMUL 3 NI 7(NI 2+) FORMUL 9 MBY C12 H15 N3 O4 S FORMUL 10 TRS C4 H12 N O3 1+ FORMUL 12 HOH *281(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 SER A 220 LYS A 224 1 5 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 THR A 246 ILE A 250 5 5 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 8 ILE A 68 LYS A 70 0 SHEET 2 A 8 VAL A 29 CYS A 36 1 N CYS A 36 O GLY A 69 SHEET 3 A 8 LYS A 3 HIS A 9 1 N LYS A 3 O ASN A 30 SHEET 4 A 8 VAL A 132 VAL A 136 1 O THR A 133 N THR A 4 SHEET 5 A 8 VAL A 158 MET A 164 1 O VAL A 162 N VAL A 136 SHEET 6 A 8 CYS A 205 PHE A 208 1 O PHE A 208 N ILE A 163 SHEET 7 A 8 VAL A 305 ARG A 309 1 O ALA A 308 N LEU A 207 SHEET 8 A 8 THR A 275 VAL A 279 -1 N VAL A 279 O VAL A 305 SHEET 1 B 2 VAL A 218 ARG A 219 0 SHEET 2 B 2 ALA A 256 TYR A 257 -1 O TYR A 257 N VAL A 218 SSBOND 1 CYS A 199 CYS A 304 1555 1555 2.08 LINK NI B NI A 406 O1 BTRS A 409 1555 1555 1.82 LINK NI NI A 402 O HOH A 661 1555 1555 1.85 LINK NI NI A 402 O HOH A 751 1555 1555 1.90 LINK NI NI A 404 O HOH A 725 1555 1555 1.91 LINK NI B NI A 406 O HOH A 742 1555 1555 1.91 LINK NI NI A 407 O HOH A 729 1555 1555 1.94 LINK N SER A -1 NI NI A 405 1555 1555 1.95 LINK ND1 HIS A 0 NI NI A 405 1555 1555 1.97 LINK NI NI A 407 O HOH A 728 1555 1555 2.01 LINK N HIS A 0 NI NI A 405 1555 1555 2.05 LINK OD2 ASP A 190 NI NI A 407 1555 1555 2.07 LINK NI B NI A 406 N BTRS A 409 1555 1555 2.09 LINK NE2 HIS A 58 NI NI A 402 1555 1555 2.09 LINK NE2 HIS A 115 NI NI A 403 1555 1555 2.12 LINK NI NI A 407 O HOH A 780 1555 1555 2.15 LINK OD2BASP A 14 NI B NI A 406 1555 1555 2.18 LINK N GLY A -2 NI NI A 405 1555 1555 2.19 LINK NI A NI A 410 O HOH A 757 1555 1555 2.22 LINK NI B NI A 406 O3 BTRS A 409 1555 1555 2.23 LINK NI NI A 402 O HOH A 704 1555 1555 2.24 LINK NI NI A 407 O HOH A 755 1555 1555 2.28 LINK NI NI A 404 O HOH A 772 1555 1555 2.29 LINK NE2 HIS A 247 NI B NI A 410 1555 1555 2.31 LINK O THR A 137 CA CA A 401 1555 1555 2.32 LINK OD1 ASP A 10 CA CA A 401 1555 1555 2.33 LINK CA CA A 401 O HOH A 742 1555 1555 2.34 LINK OD2 ASP A 261 CA CA A 401 1555 1555 2.42 LINK OD2 ASP A 15 CA CA A 401 1555 1555 2.47 LINK CA CA A 401 O2'AMBY A 408 1555 1555 2.53 LINK OD1 ASP A 15 CA CA A 401 1555 1555 2.57 LINK CA CA A 401 O HOH A 527 1555 1555 2.58 LINK CA CA A 401 O3'AMBY A 408 1555 1555 2.74 LINK NI NI A 407 O HOH A 540 1555 1555 2.77 LINK NE2 HIS A 317 NI NI A 404 1555 1555 2.77 LINK NE2 HIS A 247 NI A NI A 410 1555 1555 2.77 LINK CA CA A 401 O1 BTRS A 409 1555 1555 2.80 SITE 1 AC1 9 ASP A 10 ASP A 15 THR A 137 ASP A 261 SITE 2 AC1 9 NI A 406 MBY A 408 TRS A 409 HOH A 527 SITE 3 AC1 9 HOH A 742 SITE 1 AC2 6 HIS A 58 HOH A 661 HOH A 696 HOH A 704 SITE 2 AC2 6 HOH A 751 HOH A 764 SITE 1 AC3 6 HIS A 115 HOH A 639 HOH A 735 HOH A 737 SITE 2 AC3 6 HOH A 765 HOH A 766 SITE 1 AC4 5 HIS A 317 HOH A 541 HOH A 703 HOH A 725 SITE 2 AC4 5 HOH A 772 SITE 1 AC5 4 GLY A -2 SER A -1 HIS A 0 MET A 1 SITE 1 AC6 5 ASP A 14 ASP A 40 CA A 401 TRS A 409 SITE 2 AC6 5 HOH A 742 SITE 1 AC7 6 ASP A 190 HOH A 540 HOH A 728 HOH A 729 SITE 2 AC7 6 HOH A 755 HOH A 780 SITE 1 AC8 20 ASN A 12 ASP A 14 ASP A 15 ASP A 40 SITE 2 AC8 20 PHE A 79 TRP A 83 THR A 137 MET A 164 SITE 3 AC8 20 ASN A 173 GLU A 184 TRP A 185 ASN A 186 SITE 4 AC8 20 GLU A 248 GLU A 249 TRP A 260 ASP A 261 SITE 5 AC8 20 CA A 401 HOH A 527 HOH A 607 HOH A 742 SITE 1 AC9 15 ASP A 14 ASP A 40 PHE A 79 THR A 137 SITE 2 AC9 15 MET A 164 ASN A 173 GLU A 184 TRP A 185 SITE 3 AC9 15 ASN A 186 TRP A 260 ASP A 261 CA A 401 SITE 4 AC9 15 NI A 406 HOH A 527 HOH A 742 SITE 1 BC1 4 GLU A 82 HIS A 247 HOH A 720 HOH A 757 CRYST1 60.120 69.420 130.230 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 0.016633 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014405 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007679 0.00000