HEADER OXIDOREDUCTASE 22-JAN-15 2MYG TITLE SOLUTION STRUCTURE OF THE DITHIOLIC GLUTAREDOXIN 2-C-GRX1 FROM THE TITLE 2 PATHOGEN TRYPANOSOMA BRUCEI BRUCEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DITHIOL GLUTAREDOXIN 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 STRAIN: MHOM/CI/86/DAL972; SOURCE 5 GENE: GRX1, TBGDAL_XI1450; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-TRX1B KEYWDS GLUTAREDOXIN, TRYPANOTHIONE, TRYPANOSOMES, ELECTRON TRANSPORT, KEYWDS 2 OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.STURLESE,M.STEFANI,B.MANTA,S.MAMMI,M.COMINI,M.BELLANDA REVDAT 2 01-MAY-24 2MYG 1 REMARK SEQADV REVDAT 1 10-FEB-16 2MYG 0 JRNL AUTH M.STURLESE,M.LELLI,B.MANTA,S.MAMMI,M.A.COMINI,M.BELLANDA JRNL TITL SOLUTION STRUCTURE OF THE DITHIOLIC GLUTAREDOXIN 2-C-GRX1 JRNL TITL 2 FROM THE PATHOGEN TRYPANOSOMA BRUCEI BRUCEI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, AMBER, X-PLOR NIH REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS USING REMARK 3 AMPS-NMR SERVER REMARK 4 REMARK 4 2MYG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000104196. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 50 MM SODIUM PHOSPHATE-1, 150 MM REMARK 210 SODIUM CHLORIDE-2, 10 MM DTT-3, REMARK 210 1 MM EDTA-4, 0.05 % SODIUM AZIDE- REMARK 210 5, 0.2 MM PMSF-6, 1 MM [U-13C; U- REMARK 210 15N] TB 2-C-GRX1-7, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HNCO; 3DHN(CA)CO; REMARK 210 3D CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D H(CCO)NH; 2D (H) REMARK 210 CB(CGCC)H-TOCSY (PHE-OPTIMIZED); REMARK 210 2D (H)CB(CGCC)H-TOCSY (TYR- REMARK 210 OPTIMIZED); 2D (H)CB(CGCC)H- REMARK 210 TOCSY (HIS-OPTIMIZED); 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, UNIO'10, CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 2 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 HIS A 34 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 6 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 10 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 13 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 17 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 17 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 55 NE - CZ - NH1 ANGL. DEV. = 3.3 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 1 SER A 5 -147.89 -151.18 REMARK 500 1 ASP A 39 42.94 -105.83 REMARK 500 2 GLU A 65 -18.03 -142.18 REMARK 500 2 ASN A 73 29.75 48.05 REMARK 500 4 MET A 3 77.87 -119.98 REMARK 500 4 SER A 5 -151.18 -108.79 REMARK 500 4 ASP A 39 43.59 -84.05 REMARK 500 4 GLU A 65 -34.46 -141.81 REMARK 500 5 SER A 5 -159.65 -150.75 REMARK 500 5 ASP A 39 40.07 -84.76 REMARK 500 5 MET A 48 18.53 59.30 REMARK 500 5 GLU A 65 -13.92 -142.50 REMARK 500 6 SER A 5 -151.81 -80.61 REMARK 500 7 SER A 5 -154.66 -145.84 REMARK 500 7 ASP A 39 43.55 -84.50 REMARK 500 8 ALA A 2 -153.78 51.30 REMARK 500 8 ASP A 39 40.76 -105.07 REMARK 500 9 ASP A 39 47.56 -77.33 REMARK 500 10 PRO A 4 124.26 -31.71 REMARK 500 10 ASP A 39 27.82 -78.35 REMARK 500 10 GLU A 65 -24.33 -141.35 REMARK 500 11 MET A 3 78.23 -113.43 REMARK 500 11 VAL A 45 33.32 -76.08 REMARK 500 12 SER A 5 -152.21 -110.75 REMARK 500 12 ASP A 39 48.16 -85.44 REMARK 500 12 VAL A 45 44.81 -79.76 REMARK 500 12 ASP A 46 -27.30 -145.84 REMARK 500 13 VAL A 45 36.73 -78.26 REMARK 500 15 ASP A 39 38.52 -93.06 REMARK 500 15 GLU A 65 -33.17 -142.39 REMARK 500 16 SER A 5 -161.57 -107.52 REMARK 500 17 SER A 5 -152.00 57.44 REMARK 500 18 SER A 49 2.14 -63.76 REMARK 500 18 GLU A 50 13.69 -143.98 REMARK 500 19 ASP A 39 48.09 -79.26 REMARK 500 19 SER A 49 20.31 -74.87 REMARK 500 19 GLU A 50 10.26 -150.24 REMARK 500 19 TYR A 62 -1.41 -140.40 REMARK 500 19 GLU A 65 -25.10 -142.27 REMARK 500 20 ALA A 2 -3.45 -142.65 REMARK 500 20 MET A 3 77.43 -113.76 REMARK 500 20 ASP A 39 37.10 -85.97 REMARK 500 20 VAL A 45 40.34 -80.31 REMARK 500 20 ASP A 46 -30.82 -141.92 REMARK 500 20 GLU A 65 -20.22 -142.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 10 TYR A 25 0.07 SIDE CHAIN REMARK 500 13 TYR A 62 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25451 RELATED DB: BMRB DBREF 2MYG A 3 97 UNP E7AIJ0 E7AIJ0_9TRYP 1 95 SEQADV 2MYG GLY A 1 UNP E7AIJ0 EXPRESSION TAG SEQADV 2MYG ALA A 2 UNP E7AIJ0 EXPRESSION TAG SEQRES 1 A 97 GLY ALA MET PRO SER ILE ALA SER MET ILE LYS GLY ASN SEQRES 2 A 97 LYS VAL VAL VAL PHE SER TRP VAL THR CYS PRO TYR CYS SEQRES 3 A 97 VAL ARG ALA GLU LYS LEU LEU HIS ALA ARG THR LYS ASP SEQRES 4 A 97 ILE THR VAL HIS TYR VAL ASP LYS MET SER GLU GLY GLU SEQRES 5 A 97 GLN LEU ARG GLY GLU ILE TYR GLN ALA TYR LYS HIS GLU SEQRES 6 A 97 THR VAL PRO ALA ILE PHE ILE ASN GLY ASN PHE ILE GLY SEQRES 7 A 97 GLY CYS SER ASP LEU GLU ALA LEU ASP LYS GLU GLY LYS SEQRES 8 A 97 LEU ASP GLY LEU LEU SER HELIX 1 1 SER A 5 GLY A 12 5 8 HELIX 2 2 CYS A 23 THR A 37 1 15 HELIX 3 3 GLU A 50 LYS A 63 1 14 HELIX 4 4 GLY A 79 LYS A 88 1 10 HELIX 5 5 LYS A 91 LEU A 96 1 6 SHEET 1 A 4 ILE A 40 TYR A 44 0 SHEET 2 A 4 VAL A 15 SER A 19 1 N VAL A 17 O HIS A 43 SHEET 3 A 4 ALA A 69 ILE A 72 -1 O ALA A 69 N PHE A 18 SHEET 4 A 4 ASN A 75 ILE A 77 -1 O ILE A 77 N ILE A 70 CISPEP 1 VAL A 67 PRO A 68 1 -5.99 CISPEP 2 VAL A 67 PRO A 68 2 -4.15 CISPEP 3 MET A 3 PRO A 4 3 0.74 CISPEP 4 VAL A 67 PRO A 68 3 5.27 CISPEP 5 VAL A 67 PRO A 68 4 -4.50 CISPEP 6 VAL A 67 PRO A 68 5 -2.75 CISPEP 7 VAL A 67 PRO A 68 6 -2.35 CISPEP 8 VAL A 67 PRO A 68 7 -3.25 CISPEP 9 VAL A 67 PRO A 68 8 -11.85 CISPEP 10 VAL A 67 PRO A 68 9 -9.13 CISPEP 11 VAL A 67 PRO A 68 10 -15.34 CISPEP 12 VAL A 67 PRO A 68 11 5.04 CISPEP 13 VAL A 67 PRO A 68 12 -0.08 CISPEP 14 VAL A 67 PRO A 68 13 -6.39 CISPEP 15 VAL A 67 PRO A 68 14 -3.48 CISPEP 16 VAL A 67 PRO A 68 15 -6.37 CISPEP 17 VAL A 67 PRO A 68 16 -13.35 CISPEP 18 VAL A 67 PRO A 68 17 -0.83 CISPEP 19 VAL A 67 PRO A 68 18 -3.35 CISPEP 20 VAL A 67 PRO A 68 19 -6.04 CISPEP 21 VAL A 67 PRO A 68 20 0.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1