HEADER OXIDOREDUCTASE 27-AUG-18 6AJ8 TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI GLYCOSOMAL ISOCITRATE TITLE 2 DEHYDROGENASE IN COMPLEX WITH NADP+, ALPHA-KETOGLUTARATE AND CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP]; COMPND 3 CHAIN: A, B; 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 6AJ8 1 LINK REVDAT 1 28-AUG-19 6AJ8 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 30973 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1596 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1653 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.3260 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 : 108 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : 0.83000 REMARK 3 B33 (A**2) : 0.17000 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): 0.798 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.267 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.856 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6840 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6478 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9261 ; 1.670 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14916 ; 1.066 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 830 ; 7.564 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 304 ;36.164 ;23.553 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1205 ;20.576 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;21.106 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1019 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7621 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1577 ; 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): 3317 ; 0.919 ; 2.463 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3316 ; 0.919 ; 2.461 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4148 ; 1.666 ; 3.689 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4149 ; 1.665 ; 3.692 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3523 ; 0.723 ; 2.548 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3519 ; 0.713 ; 2.541 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5110 ; 1.297 ; 3.771 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7868 ; 4.242 ;19.400 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7840 ; 4.172 ;19.341 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 413 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 4.2389 96.0287 -48.5975 REMARK 3 T TENSOR REMARK 3 T11: 0.1525 T22: 0.1092 REMARK 3 T33: 0.2255 T12: -0.0308 REMARK 3 T13: 0.1163 T23: 0.0152 REMARK 3 L TENSOR REMARK 3 L11: 1.1256 L22: 2.3211 REMARK 3 L33: 1.0755 L12: -0.1714 REMARK 3 L13: -0.0057 L23: 1.1149 REMARK 3 S TENSOR REMARK 3 S11: -0.2692 S12: 0.2007 S13: -0.3791 REMARK 3 S21: 0.3187 S22: 0.2043 S23: 0.4046 REMARK 3 S31: 0.0494 S32: -0.0031 S33: 0.0649 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 413 REMARK 3 RESIDUE RANGE : B 501 B 501 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9333 127.3260 -47.3006 REMARK 3 T TENSOR REMARK 3 T11: 0.2225 T22: 0.1294 REMARK 3 T33: 0.1655 T12: 0.0029 REMARK 3 T13: 0.0465 T23: -0.0866 REMARK 3 L TENSOR REMARK 3 L11: 0.2578 L22: 3.3747 REMARK 3 L33: 1.0725 L12: 0.3030 REMARK 3 L13: -0.0697 L23: 0.6770 REMARK 3 S TENSOR REMARK 3 S11: -0.2097 S12: 0.0197 S13: 0.0165 REMARK 3 S21: -0.3087 S22: 0.5591 S23: -0.5737 REMARK 3 S31: -0.1732 S32: 0.0139 S33: -0.3494 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 6AJ8 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_1300008879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 34871 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.54400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 6AJ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 100MM PCB BUFFER, PH REMARK 280 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 29.23700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.06800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.01050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.06800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.23700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.01050 REMARK 290 SMTRY3 4 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: 8940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL 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 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 OD1 ASP B 50 CG LYS B 89 1.07 REMARK 500 NZ LYS A 3 O PHE A 32 1.30 REMARK 500 NZ LYS A 3 C PRO A 33 1.91 REMARK 500 CG ASP B 50 CG LYS B 89 1.95 REMARK 500 OD1 ASP B 50 CB LYS B 89 2.02 REMARK 500 NZ LYS A 3 C PHE A 32 2.07 REMARK 500 OG SER B 325 O LEU B 391 2.12 REMARK 500 CE LYS A 3 O PRO A 33 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O GLN A 319 CG1 VAL A 413 4464 2.17 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 LYS B 320 N - CA - C ANGL. DEV. = -17.8 DEGREES REMARK 500 ARG B 342 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 SER B 411 N - CA - C ANGL. DEV. = -16.6 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 2 -168.50 -170.64 REMARK 500 SER A 5 76.72 59.55 REMARK 500 GLU A 17 -137.54 58.87 REMARK 500 ILE A 31 -79.34 -99.42 REMARK 500 ASN A 36 78.74 -112.13 REMARK 500 ASP A 79 -165.85 -125.25 REMARK 500 ASP A 137 -90.74 -126.92 REMARK 500 ASN A 160 -166.73 -77.26 REMARK 500 ALA A 307 35.03 -89.39 REMARK 500 ASN A 348 73.03 -108.54 REMARK 500 LYS A 383 -158.34 -97.83 REMARK 500 ASN A 384 20.11 46.95 REMARK 500 ASN B 2 -52.98 -152.05 REMARK 500 GLU B 17 -133.78 55.26 REMARK 500 PHE B 86 -163.11 -104.67 REMARK 500 LYS B 89 -70.89 -138.00 REMARK 500 ASP B 137 -127.50 54.51 REMARK 500 PHE B 170 140.48 -170.64 REMARK 500 TYR B 234 -31.59 -139.74 REMARK 500 ASN B 348 75.81 -106.88 REMARK 500 LYS B 380 98.82 -162.92 REMARK 500 GLU B 382 -71.78 -0.76 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 ILE B 379 LYS B 380 146.08 REMARK 500 LYS B 380 GLY B 381 146.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 727 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B 706 DISTANCE = 6.20 ANGSTROMS 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 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 251 OD2 REMARK 620 2 ASP B 274 O 91.8 REMARK 620 3 ASP B 274 OD1 79.4 64.8 REMARK 620 4 ASP B 278 OD2 79.8 56.7 116.4 REMARK 620 5 HOH B 685 O 98.9 156.4 137.8 104.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 274 O REMARK 620 2 ASP A 274 OD1 82.1 REMARK 620 3 ASP A 278 OD1 71.6 151.9 REMARK 620 4 ASP B 251 OD2 70.7 78.4 101.3 REMARK 620 5 HOH B 679 O 150.8 96.7 111.1 80.4 REMARK 620 N 1 2 3 4 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 CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 502 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 6AJ8 A 1 413 UNP Q387G0 Q387G0_TRYB2 1 413 DBREF 6AJ8 B 1 413 UNP Q387G0 Q387G0_TRYB2 1 413 SEQADV 6AJ8 SER A 1 UNP Q387G0 MET 1 ENGINEERED MUTATION SEQADV 6AJ8 SER B 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 B 413 SER ASN LYS ILE SER ALA THR GLY VAL LEU VAL GLU LEU SEQRES 2 B 413 ASP GLY ASP GLU MET THR ARG VAL ILE TRP LYS LYS ILE SEQRES 3 B 413 LYS GLU THR LEU ILE PHE PRO PHE VAL ASN VAL PRO ILE SEQRES 4 B 413 GLU TYR TYR ASP LEU SER MET GLU ASN ARG ASP LYS THR SEQRES 5 B 413 GLU ASP ARG VAL THR VAL GLU ALA ALA TYR ALA ILE LYS SEQRES 6 B 413 LYS HIS GLY VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 B 413 ASP GLU ALA ARG VAL LYS GLU PHE ASN LEU LYS LYS MET SEQRES 8 B 413 TRP ARG SER PRO ASN GLY THR ILE ARG THR ILE LEU GLY SEQRES 9 B 413 GLY THR VAL PHE ARG GLU PRO ILE ILE CYS SER ASN VAL SEQRES 10 B 413 PRO ARG LEU VAL THR THR TRP LYS LYS PRO VAL VAL ILE SEQRES 11 B 413 GLY ARG HIS ALA PHE GLY ASP GLN TYR SER ALA THR ASP SEQRES 12 B 413 ALA VAL VAL LYS GLU PRO GLY THR PHE GLU MET ARG PHE SEQRES 13 B 413 ILE PRO ALA ASN GLY GLY GLU PRO LYS VAL TYR LYS VAL SEQRES 14 B 413 PHE ASP TYR LYS SER GLY GLY VAL MET MET GLY MET TYR SEQRES 15 B 413 ASN THR ASP ASP SER ILE ARG ASP PHE ALA ARG SER CYS SEQRES 16 B 413 PHE GLU PHE ALA LEU ALA ARG LYS TRP PRO LEU TYR LEU SEQRES 17 B 413 SER THR LYS ASN THR ILE LEU LYS HIS TYR ASP GLY ARG SEQRES 18 B 413 PHE LYS ASP ILE PHE ALA GLU MET TYR LYS ALA LEU TYR SEQRES 19 B 413 GLU THR LYS PHE LYS THR CYS GLY ILE PHE TYR GLU HIS SEQRES 20 B 413 ARG LEU ILE ASP ASP MET VAL ALA HIS CYS MET ARG SER SEQRES 21 B 413 GLU GLY GLY TYR VAL TRP ALA CYS LYS ASN TYR ASP GLY SEQRES 22 B 413 ASP VAL GLN SER ASP SER LEU ALA GLN GLY PHE GLY SER SEQRES 23 B 413 LEU GLY MET MET THR SER ILE LEU MET THR PRO ASP GLY SEQRES 24 B 413 LYS THR VAL GLU VAL GLU ALA ALA HIS GLY THR VAL THR SEQRES 25 B 413 ARG HIS TYR ARG ASP TYR GLN LYS GLY LYS GLU THR SER SEQRES 26 B 413 THR ASN PRO VAL ALA SER ILE PHE ALA TRP THR ARG ALA SEQRES 27 B 413 LEU ALA HIS ARG ALA ARG VAL ASP ASN ASN ASN THR LEU SEQRES 28 B 413 LEU GLU PHE THR GLN ARG LEU GLU ASP VAL ILE ILE ALA SEQRES 29 B 413 THR ILE GLU ALA GLY ALA MET THR GLU ASP LEU ALA ILE SEQRES 30 B 413 CYS ILE LYS GLY GLU LYS ASN VAL VAL ARG ALA ASP TYR SEQRES 31 B 413 LEU ASN THR ASP GLU PHE ILE ASP ALA VAL SER GLN ARG SEQRES 32 B 413 LEU LYS VAL ALA MET GLN LYS SER LYS VAL HET NAP A 501 48 HET CA A 502 1 HET CA A 503 1 HET NAP B 501 48 HET AKG B 502 10 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM CA CALCIUM ION HETNAM AKG 2-OXOGLUTARIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 CA 2(CA 2+) FORMUL 7 AKG C5 H6 O5 FORMUL 8 HOH *232(H2 O) HELIX 1 AA1 ASP A 16 ILE A 31 1 16 HELIX 2 AA2 SER A 45 THR A 52 1 8 HELIX 3 AA3 ASP A 54 GLY A 68 1 15 HELIX 4 AA4 ASP A 79 ASN A 87 1 9 HELIX 5 AA5 SER A 94 GLY A 104 1 11 HELIX 6 AA6 ASP A 137 ALA A 141 5 5 HELIX 7 AA7 ASP A 185 LYS A 203 1 19 HELIX 8 AA8 HIS A 217 TYR A 234 1 18 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 GLY A 285 1 17 HELIX 12 AB3 SER A 286 GLY A 288 5 3 HELIX 13 AB4 VAL A 311 LYS A 320 1 10 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 GLY A 381 1 10 HELIX 17 AB8 VAL A 386 TYR A 390 5 5 HELIX 18 AB9 ASN A 392 GLN A 409 1 18 HELIX 19 AC1 ASP B 16 ILE B 31 1 16 HELIX 20 AC2 SER B 45 THR B 52 1 8 HELIX 21 AC3 ASP B 54 GLY B 68 1 15 HELIX 22 AC4 ASP B 79 PHE B 86 1 8 HELIX 23 AC5 SER B 94 GLY B 104 1 11 HELIX 24 AC6 GLY B 136 ALA B 141 5 6 HELIX 25 AC7 ASP B 185 LYS B 203 1 19 HELIX 26 AC8 HIS B 217 TYR B 234 1 18 HELIX 27 AC9 TYR B 234 GLY B 242 1 9 HELIX 28 AD1 ILE B 250 SER B 260 1 11 HELIX 29 AD2 LYS B 269 GLY B 285 1 17 HELIX 30 AD3 SER B 286 GLY B 288 5 3 HELIX 31 AD4 VAL B 311 TYR B 318 1 8 HELIX 32 AD5 PRO B 328 ASN B 347 1 20 HELIX 33 AD6 ASN B 348 GLY B 369 1 22 HELIX 34 AD7 THR B 372 GLY B 381 1 10 HELIX 35 AD8 GLU B 382 VAL B 385 5 4 HELIX 36 AD9 ASN B 392 GLN B 409 1 18 SHEET 1 AA110 ILE A 39 ASP A 43 0 SHEET 2 AA110 LEU A 10 ASP A 14 1 N ASP A 14 O TYR A 42 SHEET 3 AA110 VAL A 69 LYS A 72 1 O VAL A 71 N VAL A 11 SHEET 4 AA110 VAL A 302 ALA A 306 1 O VAL A 304 N GLY A 70 SHEET 5 AA110 MET A 290 MET A 295 -1 N SER A 292 O GLU A 305 SHEET 6 AA110 THR A 106 PRO A 111 -1 N PHE A 108 O ILE A 293 SHEET 7 AA110 VAL A 128 ARG A 132 -1 O ILE A 130 N ARG A 109 SHEET 8 AA110 TYR A 264 CYS A 268 1 O TRP A 266 N VAL A 129 SHEET 9 AA110 LEU A 206 THR A 210 1 N TYR A 207 O ALA A 267 SHEET 10 AA110 TYR A 245 LEU A 249 1 O ARG A 248 N LEU A 208 SHEET 1 AA2 4 THR A 142 VAL A 146 0 SHEET 2 AA2 4 GLY A 176 THR A 184 -1 O GLY A 176 N VAL A 146 SHEET 3 AA2 4 GLY B 176 THR B 184 -1 O ASN B 183 N VAL A 177 SHEET 4 AA2 4 THR B 142 VAL B 146 -1 N THR B 142 O GLY B 180 SHEET 1 AA3 4 LYS A 165 ASP A 171 0 SHEET 2 AA3 4 GLY A 150 PRO A 158 -1 N MET A 154 O TYR A 167 SHEET 3 AA3 4 GLY B 150 PRO B 158 -1 O ARG B 155 N GLU A 153 SHEET 4 AA3 4 LYS B 165 TYR B 172 -1 O PHE B 170 N PHE B 152 SHEET 1 AA4 2 ILE B 4 SER B 5 0 SHEET 2 AA4 2 VAL B 35 ASN B 36 1 O ASN B 36 N ILE B 4 SHEET 1 AA510 ILE B 39 TYR B 42 0 SHEET 2 AA510 LEU B 10 LEU B 13 1 N GLU B 12 O TYR B 42 SHEET 3 AA510 VAL B 69 LYS B 72 1 O VAL B 69 N VAL B 11 SHEET 4 AA510 VAL B 302 ALA B 306 1 O VAL B 304 N GLY B 70 SHEET 5 AA510 MET B 290 MET B 295 -1 N SER B 292 O GLU B 305 SHEET 6 AA510 THR B 106 PRO B 111 -1 N PHE B 108 O ILE B 293 SHEET 7 AA510 VAL B 128 ARG B 132 -1 O ILE B 130 N ARG B 109 SHEET 8 AA510 TYR B 264 CYS B 268 1 O CYS B 268 N GLY B 131 SHEET 9 AA510 LEU B 206 THR B 210 1 N TYR B 207 O ALA B 267 SHEET 10 AA510 TYR B 245 LEU B 249 1 O ARG B 248 N LEU B 208 LINK OD2 ASP A 251 CA CA A 503 1555 1555 2.37 LINK O ASP A 274 CA CA A 502 1555 1555 3.01 LINK OD1 ASP A 274 CA CA A 502 1555 1555 2.88 LINK OD1 ASP A 278 CA CA A 502 1555 1555 2.50 LINK CA CA A 502 OD2 ASP B 251 1555 1555 2.82 LINK CA CA A 502 O HOH B 679 1555 1555 2.37 LINK CA CA A 503 O ASP B 274 1555 1555 3.02 LINK CA CA A 503 OD1 ASP B 274 1555 1555 2.33 LINK CA CA A 503 OD2 ASP B 278 1555 1555 2.46 LINK CA CA A 503 O HOH B 685 1555 1555 2.83 SITE 1 AC1 20 LYS A 72 THR A 75 ILE A 76 THR A 77 SITE 2 AC1 20 ARG A 82 ASN A 96 GLU A 305 HIS A 308 SITE 3 AC1 20 GLY A 309 THR A 310 VAL A 311 THR A 312 SITE 4 AC1 20 ARG A 313 HIS A 314 THR A 326 ASN A 327 SITE 5 AC1 20 HOH A 604 HOH A 615 HOH A 654 HOH A 664 SITE 1 AC2 4 ASP A 274 ASP A 278 ASP B 251 HOH B 679 SITE 1 AC3 4 ASP A 251 ASP B 274 ASP B 278 HOH B 685 SITE 1 AC4 16 LYS B 72 THR B 75 ILE B 76 THR B 77 SITE 2 AC4 16 ARG B 82 ASN B 96 GLU B 305 HIS B 308 SITE 3 AC4 16 GLY B 309 THR B 310 VAL B 311 THR B 312 SITE 4 AC4 16 HIS B 314 THR B 326 ASN B 327 HOH B 668 SITE 1 AC5 6 SER B 94 ASN B 96 ARG B 100 ARG B 132 SITE 2 AC5 6 HOH B 633 HOH B 661 CRYST1 58.474 112.021 132.136 90.00 90.00 90.00 P 21 21 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 0.017102 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007568 0.00000