HEADER ELECTRON TRANSPORT 02-JUL-99 1QUW TITLE SOLUTION STRUCTURE OF THE THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALICYCLOBACILLUS ACIDOCALDARIUS; SOURCE 3 ORGANISM_TAXID: 405212; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PTRC99A; SOURCE 7 OTHER_DETAILS: BACTERIUM KEYWDS ALPHA/BETA OPEN-TWISTED PROTEIN, THIOL-DISULFIDE, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.NICASTRO,C.DE CHIARA,E.PEDONE,M.TATO,M.ROSSI REVDAT 4 02-MAR-22 1QUW 1 REMARK REVDAT 3 24-FEB-09 1QUW 1 VERSN REVDAT 2 01-APR-03 1QUW 1 JRNL REVDAT 1 26-JAN-00 1QUW 0 JRNL AUTH G.NICASTRO,C.DE CHIARA,E.PEDONE,M.TATO,M.ROSSI,S.BARTOLUCCI JRNL TITL NMR SOLUTION STRUCTURE OF A NOVEL THIOREDOXIN FROM BACILLUS JRNL TITL 2 ACIDOCALDARIUS POSSIBLE DETERMINANTS OF PROTEIN STABILITY. JRNL REF EUR.J.BIOCHEM. V. 267 403 2000 JRNL REFN ISSN 0014-2956 JRNL PMID 10632710 JRNL DOI 10.1046/J.1432-1327.2000.01015.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BARTOLUCCI,A.GUAGLIARDI,E.PEDONE,D.DE PASCALE,R.CANNIO, REMARK 1 AUTH 2 L.CAMARDELLA,M.ROSSI,G.NICASTRO,C.DE CHIARA,P.FACCI, REMARK 1 AUTH 3 G.MASCETTI,C.NICOLINI REMARK 1 TITL THIOREDOXIN FROM BACILLUS ACIDOCALDARIUS: CHARACTERIZATION, REMARK 1 TITL 2 HIGH-LEVEL EXPRESSION IN E. COLI AND MOLECULAR MODELING REMARK 1 REF BIOCHEM.J. V. 328 277 1997 REMARK 1 REFN ISSN 0264-6021 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.M.PEDONE,S.BARTOLUCCI,M.ROSSI,M.SAVIANO REMARK 1 TITL COMPUTATIONAL ANALYSIS OF THE THERMAL STABILITY IN REMARK 1 TITL 2 THIOREDOXINS: A MOLECULAR DYNAMICS APPROACH REMARK 1 REF J.BIOMOL.STRUCT.DYN. V. 16 437 1998 REMARK 1 REFN ISSN 0739-1102 REMARK 1 REFERENCE 3 REMARK 1 AUTH E.PEDONE,R.CANNIO,M.SAVIANO,M.ROSSI,S.BARTOLUCCI REMARK 1 TITL PREDICTION AND EXPERIMENTAL TESTING OF THE BACILLUS REMARK 1 TITL 2 ACIDOCALDARIUS THIOREDOXIN STABILITY REMARK 1 REF BIOCHEM.J. V. 339 309 1999 REMARK 1 REFN ISSN 0264-6021 REMARK 1 DOI 10.1042/0264-6021:3390309 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 4.1, DISCOVER 95 REMARK 3 AUTHORS : VARIAN (VNMR), BIOSYM (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE ARE BASED ON A TOTAL OF 2276 NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, REMARK 3 99 DIHEDRAL ANGLE RESTRAINTS. REMARK 4 REMARK 4 1QUW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-99. REMARK 100 THE DEPOSITION ID IS D_1000009284. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 308 REMARK 210 PH : 5.8; 5.8 REMARK 210 IONIC STRENGTH : 50MM BUFFER PHOSPHATE; 50MM REMARK 210 BUFFER PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM RECOMBINANT THIOREDOXIN REMARK 210 FROM BACILLUS ACIDOCALDARIUS; REMARK 210 50MM PHOSPHATE BUFFER NA; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D NOESY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX FELIX95, DISCOVER 95 REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINED REMARK 210 MOLECULAR DYNAMICS AND REMARK 210 RESTRAINED ENERGY MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 O THR A 6 H PHE A 10 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 HIS A 46 CG HIS A 46 CD2 0.056 REMARK 500 2 HIS A 46 CG HIS A 46 CD2 0.054 REMARK 500 4 HIS A 46 CG HIS A 46 CD2 0.055 REMARK 500 5 HIS A 46 CG HIS A 46 CD2 0.058 REMARK 500 6 HIS A 46 CG HIS A 46 CD2 0.056 REMARK 500 7 HIS A 46 CG HIS A 46 CD2 0.057 REMARK 500 8 HIS A 46 CG HIS A 46 CD2 0.055 REMARK 500 9 HIS A 46 CG HIS A 46 CD2 0.054 REMARK 500 10 HIS A 46 CG HIS A 46 CD2 0.056 REMARK 500 11 HIS A 46 CG HIS A 46 CD2 0.054 REMARK 500 12 HIS A 46 CG HIS A 46 CD2 0.057 REMARK 500 13 HIS A 46 CG HIS A 46 CD2 0.055 REMARK 500 14 HIS A 46 CG HIS A 46 CD2 0.056 REMARK 500 15 HIS A 46 CG HIS A 46 CD2 0.055 REMARK 500 18 HIS A 46 CG HIS A 46 CD2 0.055 REMARK 500 19 HIS A 46 CG HIS A 46 CD2 0.055 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 1 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 2 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 4 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 5 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 6 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 7 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 8 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 9 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 10 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 11 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 12 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 13 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 14 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 15 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 16 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 17 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 18 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 19 HIS A 46 ND1 - CE1 - NE2 ANGL. DEV. = 8.0 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 ASP A 7 -56.97 -24.91 REMARK 500 1 ASP A 17 84.67 -172.38 REMARK 500 1 ALA A 47 -70.05 69.96 REMARK 500 1 ASP A 48 35.12 -87.50 REMARK 500 1 LYS A 49 -48.30 -153.64 REMARK 500 2 ASP A 17 -51.39 -162.57 REMARK 500 2 ALA A 47 -83.81 68.54 REMARK 500 2 ASP A 48 37.45 -87.42 REMARK 500 2 LYS A 49 -42.13 -145.11 REMARK 500 2 LYS A 79 -71.35 -91.92 REMARK 500 2 ARG A 82 118.10 -161.68 REMARK 500 2 PRO A 92 166.86 -49.11 REMARK 500 3 ASP A 17 -65.72 -158.34 REMARK 500 3 ALA A 47 -92.90 63.63 REMARK 500 3 PRO A 92 171.48 -57.97 REMARK 500 4 ASP A 7 -54.42 -25.93 REMARK 500 4 ASP A 17 -60.67 -166.88 REMARK 500 4 ALA A 47 -88.05 60.91 REMARK 500 4 ASP A 48 43.04 -79.11 REMARK 500 4 LYS A 49 -56.88 -153.49 REMARK 500 4 LYS A 79 -75.05 -110.49 REMARK 500 4 PRO A 92 158.03 -48.81 REMARK 500 5 ASP A 17 -46.90 -164.60 REMARK 500 5 ALA A 47 -74.72 68.86 REMARK 500 5 LYS A 49 -46.62 -142.00 REMARK 500 5 LYS A 79 -76.49 -100.31 REMARK 500 5 PRO A 92 172.27 -53.49 REMARK 500 6 ASP A 17 -67.09 -167.55 REMARK 500 6 ALA A 47 -85.41 66.99 REMARK 500 6 ASP A 48 36.07 -84.92 REMARK 500 6 LYS A 49 -35.67 -148.05 REMARK 500 7 ASP A 17 -50.35 -165.14 REMARK 500 7 ALA A 47 -83.43 68.29 REMARK 500 7 ASP A 48 32.67 -79.03 REMARK 500 7 LYS A 49 -45.18 -154.16 REMARK 500 7 SER A 71 119.42 -163.64 REMARK 500 7 LYS A 79 -72.92 -130.47 REMARK 500 7 PRO A 92 164.20 -47.74 REMARK 500 8 ASP A 17 -57.21 -165.16 REMARK 500 8 ALA A 47 -69.41 71.04 REMARK 500 8 LYS A 49 -40.70 -145.35 REMARK 500 8 SER A 71 127.45 -170.42 REMARK 500 8 LYS A 79 -76.03 -94.83 REMARK 500 9 ASP A 17 -69.52 -159.33 REMARK 500 9 ALA A 47 -79.65 69.43 REMARK 500 9 LYS A 49 -40.89 -141.29 REMARK 500 9 LYS A 79 -75.11 -106.47 REMARK 500 10 ASP A 17 -59.28 -164.10 REMARK 500 10 ALA A 47 -82.81 65.74 REMARK 500 10 ASP A 48 36.19 -85.90 REMARK 500 REMARK 500 THIS ENTRY HAS 105 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1QUW A 1 105 UNP P80579 THIO_ALIAC 1 105 SEQRES 1 A 105 ALA THR MET THR LEU THR ASP ALA ASN PHE GLN GLN ALA SEQRES 2 A 105 ILE GLN GLY ASP LYS PRO VAL LEU VAL ASP PHE TRP ALA SEQRES 3 A 105 ALA TRP CYS GLY PRO CYS ARG MET MET ALA PRO VAL LEU SEQRES 4 A 105 GLU GLU PHE ALA GLU ALA HIS ALA ASP LYS VAL THR VAL SEQRES 5 A 105 ALA LYS LEU ASN VAL ASP GLU ASN PRO GLU THR THR SER SEQRES 6 A 105 GLN PHE GLY ILE MET SER ILE PRO THR LEU ILE LEU PHE SEQRES 7 A 105 LYS GLY GLY ARG PRO VAL LYS GLN LEU ILE GLY TYR GLN SEQRES 8 A 105 PRO LYS GLU GLN LEU GLU ALA GLN LEU ALA ASP VAL LEU SEQRES 9 A 105 GLN HELIX 1 1 THR A 6 GLN A 15 1 10 HELIX 2 2 PRO A 31 HIS A 46 1 16 HELIX 3 3 PRO A 61 GLY A 68 1 8 HELIX 4 4 PRO A 92 GLN A 105 1 14 SHEET 1 A 4 VAL A 52 ASN A 56 0 SHEET 2 A 4 VAL A 20 TRP A 25 1 O LEU A 21 N ALA A 53 SHEET 3 A 4 THR A 74 PHE A 78 -1 O THR A 74 N PHE A 24 SHEET 4 A 4 PRO A 83 ILE A 88 -1 N VAL A 84 O LEU A 77 SSBOND 1 CYS A 29 CYS A 32 1555 1555 2.00 CISPEP 1 ILE A 72 PRO A 73 1 2.21 CISPEP 2 ILE A 72 PRO A 73 2 3.33 CISPEP 3 ILE A 72 PRO A 73 3 4.30 CISPEP 4 ILE A 72 PRO A 73 4 2.99 CISPEP 5 ILE A 72 PRO A 73 5 1.23 CISPEP 6 ILE A 72 PRO A 73 6 4.67 CISPEP 7 ILE A 72 PRO A 73 7 5.55 CISPEP 8 ILE A 72 PRO A 73 8 2.93 CISPEP 9 ILE A 72 PRO A 73 9 4.95 CISPEP 10 ILE A 72 PRO A 73 10 1.19 CISPEP 11 ILE A 72 PRO A 73 11 3.11 CISPEP 12 ILE A 72 PRO A 73 12 5.72 CISPEP 13 ILE A 72 PRO A 73 13 5.39 CISPEP 14 ILE A 72 PRO A 73 14 7.97 CISPEP 15 ILE A 72 PRO A 73 15 4.86 CISPEP 16 ILE A 72 PRO A 73 16 2.56 CISPEP 17 ILE A 72 PRO A 73 17 2.67 CISPEP 18 ILE A 72 PRO A 73 18 6.27 CISPEP 19 ILE A 72 PRO A 73 19 2.80 CISPEP 20 ILE A 72 PRO A 73 20 1.37 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