HEADER OXIDOREDUCTASE 27-AUG-18 6AJ6 TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GLYCOSOMAL ISOCITRATE TITLE 2 DEHYDROGENASE IN COMPLEX WITH NADP+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP]; COMPND 3 CHAIN: A, C; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 5702; SOURCE 4 STRAIN: ILTAT 1.4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-SUMO KEYWDS TRYPANOSOMA BRUCEI, GLYCOSOME, METABOLISM, ISOCITRATE DEHYDROGENASE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,D.K.INAOKA,T.SHIBA,E.O.BALOGUN,N.ZIEBART,S.ALLMAN,Y.WATANABE, AUTHOR 2 T.NOZAKI,M.BOSHART,F.BRINGAUD,S.HARADA,K.KITA REVDAT 2 22-NOV-23 6AJ6 1 REMARK REVDAT 1 28-AUG-19 6AJ6 0 JRNL AUTH X.WANG,D.K.INAOKA,T.SHIBA,E.O.BALOGUN,N.ZIEBART,S.ALLMAN, JRNL AUTH 2 Y.WATANABE,T.NOZAKI,M.BOSHART,F.BRINGAUD,S.HARADA,K.KITA JRNL TITL BIOCHEMICAL CHARACTERIZATION OF A NOVEL TRYPANOSOMA BRUCEI JRNL TITL 2 GLYCOSOMAL ISOCITRATE DEHYDROGENASE WITH DUAL COENZYME JRNL TITL 3 SPECIFICITY (NADP+/NAD+) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 83.9 REMARK 3 NUMBER OF REFLECTIONS : 11582 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.309 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 558 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 253 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 25.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2620 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 20.92000 REMARK 3 B22 (A**2) : -17.14000 REMARK 3 B33 (A**2) : -3.79000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 26.33000 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): 0.171 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.440 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.305 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.902 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.817 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6804 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6466 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9208 ; 1.875 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14888 ; 1.138 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 824 ;10.410 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 300 ;38.716 ;23.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1204 ;22.999 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;16.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1018 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7548 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1564 ; 0.002 ; 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): 3302 ; 4.593 ; 7.136 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3301 ; 4.592 ; 7.134 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4124 ; 7.735 ;10.678 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4125 ; 7.734 ;10.681 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3502 ; 3.682 ; 7.416 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3503 ; 3.682 ; 7.416 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5085 ; 6.317 ;10.983 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8232 ;11.723 ;57.140 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8233 ;11.722 ;57.144 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.609 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H,-K,-L REMARK 3 TWIN FRACTION : 0.391 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 413 REMARK 3 ORIGIN FOR THE GROUP (A): 26.8163 -1.1513 17.7130 REMARK 3 T TENSOR REMARK 3 T11: 0.1671 T22: 0.1136 REMARK 3 T33: 0.0509 T12: -0.0096 REMARK 3 T13: -0.0685 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 0.3735 L22: 1.2718 REMARK 3 L33: 0.0133 L12: 0.6421 REMARK 3 L13: 0.0528 L23: 0.0822 REMARK 3 S TENSOR REMARK 3 S11: -0.0688 S12: 0.1068 S13: -0.0792 REMARK 3 S21: 0.1104 S22: 0.1133 S23: -0.2108 REMARK 3 S31: -0.0198 S32: -0.0038 S33: -0.0445 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 6AJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300008878. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-15 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 : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14385 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.79900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.450 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: 1T0L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200MM POTASSIUM NITRATE, REMARK 280 PH 7.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 54.87700 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: 8100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 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 SG CYS C 73 ND2 ASN C 96 1.78 REMARK 500 OG1 THR A 52 O ASP A 54 1.85 REMARK 500 NH2 ARG C 82 O3D NAP C 501 2.07 REMARK 500 O HIS C 341 CG2 VAL C 345 2.10 REMARK 500 NH1 ARG A 82 OE2 GLU A 85 2.11 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 GLU A 53 N - CA - C ANGL. DEV. = -17.0 DEGREES REMARK 500 ARG A 55 N - CA - C ANGL. DEV. = 16.9 DEGREES REMARK 500 LYS A 90 N - CA - C ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG C 55 N - CA - C ANGL. DEV. = 19.4 DEGREES REMARK 500 ASP C 137 N - CA - C ANGL. DEV. = -22.9 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 3 -174.49 -60.71 REMARK 500 ASP A 14 129.05 -26.42 REMARK 500 GLU A 17 -138.19 65.01 REMARK 500 GLU A 28 -62.39 -90.64 REMARK 500 ILE A 31 -89.18 -74.87 REMARK 500 VAL A 37 143.83 -177.81 REMARK 500 ASP A 54 114.11 76.60 REMARK 500 LYS A 65 -69.77 -24.51 REMARK 500 LYS A 72 -66.31 170.30 REMARK 500 CYS A 73 44.52 27.14 REMARK 500 ILE A 76 15.93 -150.44 REMARK 500 THR A 77 98.32 -27.02 REMARK 500 PRO A 78 -172.85 -65.13 REMARK 500 MET A 91 -66.36 77.71 REMARK 500 TRP A 92 -36.43 69.37 REMARK 500 ARG A 93 -162.81 72.17 REMARK 500 ARG A 100 -39.74 -36.96 REMARK 500 HIS A 133 -73.73 -76.27 REMARK 500 ALA A 134 89.48 74.67 REMARK 500 PHE A 135 151.37 135.42 REMARK 500 ASP A 137 -115.90 -107.14 REMARK 500 ALA A 141 91.34 -164.84 REMARK 500 PRO A 158 -175.26 -64.43 REMARK 500 GLU A 163 125.10 -34.43 REMARK 500 PHE A 170 142.97 -174.16 REMARK 500 SER A 174 131.35 176.44 REMARK 500 MET A 179 128.67 -175.26 REMARK 500 CYS A 195 -73.17 -41.34 REMARK 500 LEU A 215 89.73 -154.53 REMARK 500 ASP A 224 -76.12 -61.52 REMARK 500 TYR A 234 -74.76 -134.18 REMARK 500 GLU A 235 -75.91 2.46 REMARK 500 ALA A 307 -84.03 -60.50 REMARK 500 HIS A 308 155.86 -33.53 REMARK 500 ARG A 316 -53.69 -25.99 REMARK 500 ASP A 317 -88.75 -69.24 REMARK 500 TYR A 318 -105.35 41.70 REMARK 500 LYS A 320 -12.37 -49.94 REMARK 500 GLU A 323 179.05 -45.07 REMARK 500 THR A 326 132.02 -37.52 REMARK 500 THR A 365 -68.67 -18.72 REMARK 500 ASN A 392 -179.41 -67.39 REMARK 500 LYS A 410 3.81 -68.19 REMARK 500 GLU C 17 -138.98 65.59 REMARK 500 ILE C 31 -74.65 -91.77 REMARK 500 VAL C 37 82.73 -153.00 REMARK 500 ASP C 54 -132.06 62.42 REMARK 500 LYS C 72 -64.54 155.57 REMARK 500 CYS C 73 70.80 19.72 REMARK 500 ILE C 76 3.20 -150.10 REMARK 500 REMARK 500 THIS ENTRY HAS 70 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 71 LYS A 72 149.75 REMARK 500 GLY A 105 THR A 106 -147.75 REMARK 500 GLY A 136 ASP A 137 146.77 REMARK 500 TYR A 139 SER A 140 148.66 REMARK 500 LYS A 320 GLY A 321 141.71 REMARK 500 ASN C 36 VAL C 37 -146.52 REMARK 500 VAL C 71 LYS C 72 143.65 REMARK 500 ALA C 159 ASN C 160 149.75 REMARK 500 THR C 310 VAL C 311 -148.29 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP C 501 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE WAS DERIVED FROM TRYPANOSOME BRUCEI BRUCEI ILTAT 1.4. REMARK 999 HOWEVER, THE SEQUENCE REFERENCE AVAILABLE AT UNIPROT AT THE TIME OF REMARK 999 DATA PROCESSING WAS DERIVED FROM A DIFFERENT STRAIN TRYPANOSOMA REMARK 999 BRUCEI BRUCEI (STRAIN 927/4 GUTAT10.1) (TAXONOMY ID 185431). DBREF 6AJ6 A 1 413 UNP Q387G0 Q387G0_TRYB2 1 413 DBREF 6AJ6 C 1 413 UNP Q387G0 Q387G0_TRYB2 1 413 SEQADV 6AJ6 SER A 1 UNP Q387G0 MET 1 ENGINEERED MUTATION SEQADV 6AJ6 SER C 1 UNP Q387G0 MET 1 ENGINEERED MUTATION SEQRES 1 A 413 SER ASN LYS ILE SER ALA THR GLY VAL LEU VAL GLU LEU SEQRES 2 A 413 ASP GLY ASP GLU MET THR ARG VAL ILE TRP LYS LYS ILE SEQRES 3 A 413 LYS GLU THR LEU ILE PHE PRO PHE VAL ASN VAL PRO ILE SEQRES 4 A 413 GLU TYR TYR ASP LEU SER MET GLU ASN ARG ASP LYS THR SEQRES 5 A 413 GLU ASP ARG VAL THR VAL GLU ALA ALA TYR ALA ILE LYS SEQRES 6 A 413 LYS HIS GLY VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 413 ASP GLU ALA ARG VAL LYS GLU PHE ASN LEU LYS LYS MET SEQRES 8 A 413 TRP ARG SER PRO ASN GLY THR ILE ARG THR ILE LEU GLY SEQRES 9 A 413 GLY THR VAL PHE ARG GLU PRO ILE ILE CYS SER ASN VAL SEQRES 10 A 413 PRO ARG LEU VAL THR THR TRP LYS LYS PRO VAL VAL ILE SEQRES 11 A 413 GLY ARG HIS ALA PHE GLY ASP GLN TYR SER ALA THR ASP SEQRES 12 A 413 ALA VAL VAL LYS GLU PRO GLY THR PHE GLU MET ARG PHE SEQRES 13 A 413 ILE PRO ALA ASN GLY GLY GLU PRO LYS VAL TYR LYS VAL SEQRES 14 A 413 PHE ASP TYR LYS SER GLY GLY VAL MET MET GLY MET TYR SEQRES 15 A 413 ASN THR ASP ASP SER ILE ARG ASP PHE ALA ARG SER CYS SEQRES 16 A 413 PHE GLU PHE ALA LEU ALA ARG LYS TRP PRO LEU TYR LEU SEQRES 17 A 413 SER THR LYS ASN THR ILE LEU LYS HIS TYR ASP GLY ARG SEQRES 18 A 413 PHE LYS ASP ILE PHE ALA GLU MET TYR LYS ALA LEU TYR SEQRES 19 A 413 GLU THR LYS PHE LYS THR CYS GLY ILE PHE TYR GLU HIS SEQRES 20 A 413 ARG LEU ILE ASP ASP MET VAL ALA HIS CYS MET ARG SER SEQRES 21 A 413 GLU GLY GLY TYR VAL TRP ALA CYS LYS ASN TYR ASP GLY SEQRES 22 A 413 ASP VAL GLN SER ASP SER LEU ALA GLN GLY PHE GLY SER SEQRES 23 A 413 LEU GLY MET MET THR SER ILE LEU MET THR PRO ASP GLY SEQRES 24 A 413 LYS THR VAL GLU VAL GLU ALA ALA HIS GLY THR VAL THR SEQRES 25 A 413 ARG HIS TYR ARG ASP TYR GLN LYS GLY LYS GLU THR SER SEQRES 26 A 413 THR ASN PRO VAL ALA SER ILE PHE ALA TRP THR ARG ALA SEQRES 27 A 413 LEU ALA HIS ARG ALA ARG VAL ASP ASN ASN ASN THR LEU SEQRES 28 A 413 LEU GLU PHE THR GLN ARG LEU GLU ASP VAL ILE ILE ALA SEQRES 29 A 413 THR ILE GLU ALA GLY ALA MET THR GLU ASP LEU ALA ILE SEQRES 30 A 413 CYS ILE LYS GLY GLU LYS ASN VAL VAL ARG ALA ASP TYR SEQRES 31 A 413 LEU ASN THR ASP GLU PHE ILE ASP ALA VAL SER GLN ARG SEQRES 32 A 413 LEU LYS VAL ALA MET GLN LYS SER LYS VAL SEQRES 1 C 413 SER ASN LYS ILE SER ALA THR GLY VAL LEU VAL GLU LEU SEQRES 2 C 413 ASP GLY ASP GLU MET THR ARG VAL ILE TRP LYS LYS ILE SEQRES 3 C 413 LYS GLU THR LEU ILE PHE PRO PHE VAL ASN VAL PRO ILE SEQRES 4 C 413 GLU TYR TYR ASP LEU SER MET GLU ASN ARG ASP LYS THR SEQRES 5 C 413 GLU ASP ARG VAL THR VAL GLU ALA ALA TYR ALA ILE LYS SEQRES 6 C 413 LYS HIS GLY VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 C 413 ASP GLU ALA ARG VAL LYS GLU PHE ASN LEU LYS LYS MET SEQRES 8 C 413 TRP ARG SER PRO ASN GLY THR ILE ARG THR ILE LEU GLY SEQRES 9 C 413 GLY THR VAL PHE ARG GLU PRO ILE ILE CYS SER ASN VAL SEQRES 10 C 413 PRO ARG LEU VAL THR THR TRP LYS LYS PRO VAL VAL ILE SEQRES 11 C 413 GLY ARG HIS ALA PHE GLY ASP GLN TYR SER ALA THR ASP SEQRES 12 C 413 ALA VAL VAL LYS GLU PRO GLY THR PHE GLU MET ARG PHE SEQRES 13 C 413 ILE PRO ALA ASN GLY GLY GLU PRO LYS VAL TYR LYS VAL SEQRES 14 C 413 PHE ASP TYR LYS SER GLY GLY VAL MET MET GLY MET TYR SEQRES 15 C 413 ASN THR ASP ASP SER ILE ARG ASP PHE ALA ARG SER CYS SEQRES 16 C 413 PHE GLU PHE ALA LEU ALA ARG LYS TRP PRO LEU TYR LEU SEQRES 17 C 413 SER THR LYS ASN THR ILE LEU LYS HIS TYR ASP GLY ARG SEQRES 18 C 413 PHE LYS ASP ILE PHE ALA GLU MET TYR LYS ALA LEU TYR SEQRES 19 C 413 GLU THR LYS PHE LYS THR CYS GLY ILE PHE TYR GLU HIS SEQRES 20 C 413 ARG LEU ILE ASP ASP MET VAL ALA HIS CYS MET ARG SER SEQRES 21 C 413 GLU GLY GLY TYR VAL TRP ALA CYS LYS ASN TYR ASP GLY SEQRES 22 C 413 ASP VAL GLN SER ASP SER LEU ALA GLN GLY PHE GLY SER SEQRES 23 C 413 LEU GLY MET MET THR SER ILE LEU MET THR PRO ASP GLY SEQRES 24 C 413 LYS THR VAL GLU VAL GLU ALA ALA HIS GLY THR VAL THR SEQRES 25 C 413 ARG HIS TYR ARG ASP TYR GLN LYS GLY LYS GLU THR SER SEQRES 26 C 413 THR ASN PRO VAL ALA SER ILE PHE ALA TRP THR ARG ALA SEQRES 27 C 413 LEU ALA HIS ARG ALA ARG VAL ASP ASN ASN ASN THR LEU SEQRES 28 C 413 LEU GLU PHE THR GLN ARG LEU GLU ASP VAL ILE ILE ALA SEQRES 29 C 413 THR ILE GLU ALA GLY ALA MET THR GLU ASP LEU ALA ILE SEQRES 30 C 413 CYS ILE LYS GLY GLU LYS ASN VAL VAL ARG ALA ASP TYR SEQRES 31 C 413 LEU ASN THR ASP GLU PHE ILE ASP ALA VAL SER GLN ARG SEQRES 32 C 413 LEU LYS VAL ALA MET GLN LYS SER LYS VAL HET NAP A 501 48 HET NAP C 501 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) HELIX 1 AA1 ASP A 16 LEU A 30 1 15 HELIX 2 AA2 SER A 45 LYS A 51 1 7 HELIX 3 AA3 VAL A 56 GLY A 68 1 13 HELIX 4 AA4 ASP A 79 LYS A 84 1 6 HELIX 5 AA5 GLU A 85 LEU A 88 5 4 HELIX 6 AA6 SER A 94 GLY A 104 1 11 HELIX 7 AA7 THR A 184 LYS A 203 1 20 HELIX 8 AA8 LEU A 215 TYR A 234 1 20 HELIX 9 AA9 TYR A 234 CYS A 241 1 8 HELIX 10 AB1 ILE A 250 SER A 260 1 11 HELIX 11 AB2 LYS A 269 PHE A 284 1 16 HELIX 12 AB3 VAL A 311 ARG A 316 1 6 HELIX 13 AB4 ASP A 317 GLY A 321 5 5 HELIX 14 AB5 PRO A 328 ASN A 347 1 20 HELIX 15 AB6 ASN A 348 ALA A 368 1 21 HELIX 16 AB7 THR A 372 ILE A 379 1 8 HELIX 17 AB8 ASN A 392 VAL A 413 1 22 HELIX 18 AB9 ASP C 16 LEU C 30 1 15 HELIX 19 AC1 SER C 45 THR C 52 1 8 HELIX 20 AC2 VAL C 56 GLY C 68 1 13 HELIX 21 AC3 ASP C 79 LYS C 84 1 6 HELIX 22 AC4 SER C 94 LEU C 103 1 10 HELIX 23 AC5 THR C 184 ARG C 202 1 19 HELIX 24 AC6 ASP C 219 TYR C 234 1 16 HELIX 25 AC7 TYR C 234 CYS C 241 1 8 HELIX 26 AC8 ILE C 250 SER C 260 1 11 HELIX 27 AC9 LYS C 269 PHE C 284 1 16 HELIX 28 AD1 VAL C 311 ARG C 316 1 6 HELIX 29 AD2 PRO C 328 ASP C 346 1 19 HELIX 30 AD3 ASN C 349 ALA C 368 1 20 HELIX 31 AD4 THR C 372 LYS C 380 1 9 HELIX 32 AD5 ASN C 392 VAL C 413 1 22 SHEET 1 AA1 4 GLY A 70 LYS A 72 0 SHEET 2 AA1 4 VAL A 302 GLU A 305 1 O VAL A 304 N GLY A 70 SHEET 3 AA1 4 ILE A 293 MET A 295 -1 N LEU A 294 O GLU A 303 SHEET 4 AA1 4 THR A 106 PHE A 108 -1 N THR A 106 O MET A 295 SHEET 1 AA2 4 GLY A 131 ARG A 132 0 SHEET 2 AA2 4 VAL A 265 CYS A 268 1 O TRP A 266 N GLY A 131 SHEET 3 AA2 4 LEU A 206 THR A 210 1 N TYR A 207 O ALA A 267 SHEET 4 AA2 4 TYR A 245 LEU A 249 1 O GLU A 246 N LEU A 206 SHEET 1 AA3 3 ASP A 143 ALA A 144 0 SHEET 2 AA3 3 MET A 178 TYR A 182 -1 O MET A 178 N ALA A 144 SHEET 3 AA3 3 MET C 178 TYR C 182 -1 O MET C 181 N MET A 179 SHEET 1 AA4 4 LYS A 165 ASP A 171 0 SHEET 2 AA4 4 GLY A 150 PRO A 158 -1 N PHE A 152 O PHE A 170 SHEET 3 AA4 4 GLY C 150 PRO C 158 -1 O THR C 151 N ILE A 157 SHEET 4 AA4 4 VAL C 166 TYR C 172 -1 O TYR C 172 N GLY C 150 SHEET 1 AA5 5 ILE C 39 ASP C 43 0 SHEET 2 AA5 5 LEU C 10 ASP C 14 1 N GLU C 12 O TYR C 42 SHEET 3 AA5 5 VAL C 69 LYS C 72 1 O VAL C 69 N VAL C 11 SHEET 4 AA5 5 VAL C 302 ALA C 306 1 O VAL C 304 N GLY C 70 SHEET 5 AA5 5 THR C 291 MET C 295 -1 N SER C 292 O GLU C 305 SHEET 1 AA6 5 VAL C 107 PHE C 108 0 SHEET 2 AA6 5 VAL C 129 ARG C 132 -1 O ARG C 132 N VAL C 107 SHEET 3 AA6 5 VAL C 265 CYS C 268 1 O TRP C 266 N GLY C 131 SHEET 4 AA6 5 LEU C 206 THR C 210 1 N TYR C 207 O ALA C 267 SHEET 5 AA6 5 TYR C 245 LEU C 249 1 O GLU C 246 N LEU C 206 SITE 1 AC1 15 THR A 75 THR A 77 ARG A 82 ASN A 96 SITE 2 AC1 15 LEU A 287 HIS A 308 GLY A 309 THR A 310 SITE 3 AC1 15 VAL A 311 THR A 312 ARG A 313 HIS A 314 SITE 4 AC1 15 THR A 326 ASN A 327 ASP A 374 SITE 1 AC2 15 LYS A 320 THR C 75 ILE C 76 THR C 77 SITE 2 AC2 15 ARG C 82 LEU C 287 HIS C 308 GLY C 309 SITE 3 AC2 15 THR C 310 VAL C 311 THR C 312 ARG C 313 SITE 4 AC2 15 HIS C 314 THR C 326 ASN C 327 CRYST1 62.442 109.754 64.961 90.00 89.98 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 0.016015 0.000000 -0.000005 0.00000 SCALE2 0.000000 0.009111 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015394 0.00000