HEADER OXIDOREDUCTASE 24-AUG-00 1FO5 TITLE SOLUTION STRUCTURE OF REDUCED MJ0307 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THIOREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MJ0307 PROTEIN DISULFIDE OXIDOREDUCTASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_TAXID: 2190; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS DISULFIDE OXIDOREDUCTASE, THIOREDOXIN FOLD, STRUCTURAL GENOMICS, BSGC KEYWDS 2 STRUCTURE FUNDED BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY KEYWDS 3 STRUCTURAL GENOMICS CENTER, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.W.CAVE,H.S.CHO,A.M.BATCHELDER,R.KIM,H.YOKOTA,D.E.WEMMER,BERKELEY AUTHOR 2 STRUCTURAL GENOMICS CENTER (BSGC) REVDAT 6 22-MAY-24 1FO5 1 REMARK REVDAT 5 23-FEB-22 1FO5 1 REMARK REVDAT 4 24-FEB-09 1FO5 1 VERSN REVDAT 3 25-JAN-05 1FO5 1 AUTHOR KEYWDS REMARK REVDAT 2 24-AUG-04 1FO5 1 JRNL KEYWDS REMARK REVDAT 1 11-APR-01 1FO5 0 JRNL AUTH J.W.CAVE,H.S.CHO,A.M.BATCHELDER,H.YOKOTA,R.KIM,D.E.WEMMER JRNL TITL SOLUTION NUCLEAR MAGNETIC RESONANCE STRUCTURE OF A PROTEIN JRNL TITL 2 DISULFIDE OXIDOREDUCTASE FROM METHANOCOCCUS JANNASCHII. JRNL REF PROTEIN SCI. V. 10 384 2001 JRNL REFN ISSN 0961-8368 JRNL PMID 11266624 JRNL DOI 10.1110/PS.35101 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 910901, OPAL 2.6 REMARK 3 AUTHORS : BRUKER (UXNMR), LUGINBUHL ET AL. (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 505 UPPER LIMIT DISTANCE CONSTRAINTS REMARK 3 52 BACKBONE PHI TORSION ANGLE CONSTRAINTS REMARK 3 30 HYDROGEN BOND CONSTRAINTS REMARK 4 REMARK 4 1FO5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-00. REMARK 100 THE DEPOSITION ID IS D_1000011761. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 298 REMARK 210 PH : 6.3; 6.3 REMARK 210 IONIC STRENGTH : 35MM SODIUM PHOSPHATE; 35MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM MJ0307 U-15N; 35MM SODIUM REMARK 210 PHOSPHATE PH 6.3, 5 MM DTT, 0.02% REMARK 210 SODIUM AZIDE; 1.5MM MJ0307 U- REMARK 210 (15N,13C); 35MM SODIUM PHOSPHATE REMARK 210 PH 6.3, 5 MM DTT, 0.02% SODIUM REMARK 210 AZIDE; 1.5MM MJ0307; 35MM SODIUM REMARK 210 PHOSPHATE PH 6.3, 5 MM DTT, 0.02% REMARK 210 SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HMQC-J; 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, FELIX 98, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS (DYANA) REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 (OPAL) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: REMARK 210 THE STRUCTURE WAS DETERMINED USING 2D HOMONUCLEAR TECHNIQUES AND REMARK 210 TRIPLE-RESONANCE NMR SPECTROSCOPY 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 PHE A 8 HG1 THR A 9 1.60 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 TYR A 38 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 6 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 13 TYR A 38 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES REMARK 500 14 TYR A 38 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 19 VAL A 26 CG1 - CB - CG2 ANGL. DEV. = 9.9 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 1 LYS A 2 162.62 66.06 REMARK 500 1 MET A 12 -31.13 -134.62 REMARK 500 1 CYS A 13 -79.36 -77.25 REMARK 500 1 ALA A 18 -118.46 46.88 REMARK 500 1 PRO A 31 39.02 -80.01 REMARK 500 1 ASP A 32 -49.70 -178.19 REMARK 500 1 ALA A 33 48.02 -77.70 REMARK 500 1 VAL A 41 99.86 -68.13 REMARK 500 1 GLU A 43 54.56 36.69 REMARK 500 1 GLN A 46 25.72 -78.96 REMARK 500 1 GLU A 50 -119.23 -69.29 REMARK 500 1 TYR A 51 -171.68 60.59 REMARK 500 1 ASN A 62 -42.96 45.77 REMARK 500 1 THR A 72 -173.73 -58.14 REMARK 500 1 LYS A 73 39.65 -70.41 REMARK 500 1 ARG A 83 81.43 -178.53 REMARK 500 2 PHE A 8 76.41 -105.81 REMARK 500 2 MET A 12 -57.73 -122.57 REMARK 500 2 HIS A 15 15.51 46.98 REMARK 500 2 ALA A 18 -74.84 -50.35 REMARK 500 2 GLU A 29 -57.53 -121.51 REMARK 500 2 ASP A 32 -26.88 -177.78 REMARK 500 2 MET A 42 -56.17 -140.84 REMARK 500 2 ASN A 44 58.71 35.98 REMARK 500 2 MET A 54 -19.92 55.15 REMARK 500 2 ASN A 62 -36.90 51.61 REMARK 500 2 THR A 72 -163.17 -65.33 REMARK 500 2 LYS A 73 27.82 -70.79 REMARK 500 2 GLU A 74 -53.30 -29.30 REMARK 500 2 ARG A 83 -55.70 -177.62 REMARK 500 3 SER A 1 62.48 -156.91 REMARK 500 3 CYS A 13 -71.70 -80.22 REMARK 500 3 HIS A 15 -61.37 57.82 REMARK 500 3 CYS A 16 168.69 58.73 REMARK 500 3 ALA A 18 -125.41 41.37 REMARK 500 3 GLU A 25 -71.98 -52.09 REMARK 500 3 ASP A 32 -63.00 -179.14 REMARK 500 3 VAL A 36 57.41 -152.52 REMARK 500 3 MET A 42 -62.98 -153.01 REMARK 500 3 GLU A 43 11.18 -145.19 REMARK 500 3 GLN A 46 19.26 -69.25 REMARK 500 3 ASN A 62 -50.24 47.23 REMARK 500 3 THR A 72 -173.20 -60.93 REMARK 500 3 GLU A 74 -49.57 -29.35 REMARK 500 3 ARG A 83 133.41 171.25 REMARK 500 4 SER A 1 -29.70 -143.28 REMARK 500 4 LYS A 2 50.28 36.54 REMARK 500 4 CYS A 13 -60.03 132.89 REMARK 500 4 PRO A 14 -73.04 -64.77 REMARK 500 4 CYS A 16 -49.63 -146.61 REMARK 500 REMARK 500 THIS ENTRY HAS 332 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 MET A 0 SER A 1 16 -142.87 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 3 TYR A 51 0.08 SIDE CHAIN REMARK 500 4 TYR A 51 0.12 SIDE CHAIN REMARK 500 5 TYR A 51 0.12 SIDE CHAIN REMARK 500 6 ARG A 83 0.08 SIDE CHAIN REMARK 500 7 ARG A 21 0.08 SIDE CHAIN REMARK 500 12 ARG A 21 0.11 SIDE CHAIN REMARK 500 12 ARG A 83 0.13 SIDE CHAIN REMARK 500 13 ARG A 21 0.12 SIDE CHAIN REMARK 500 16 ARG A 21 0.08 SIDE CHAIN REMARK 500 16 ARG A 83 0.08 SIDE CHAIN REMARK 500 17 TYR A 51 0.11 SIDE CHAIN REMARK 500 19 TYR A 51 0.12 SIDE CHAIN REMARK 500 20 ARG A 21 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: BSGCAIR30506 RELATED DB: TARGETDB DBREF 1FO5 A 0 84 UNP Q57755 THIO_METJA 1 85 SEQRES 1 A 85 MET SER LYS VAL LYS ILE GLU LEU PHE THR SER PRO MET SEQRES 2 A 85 CYS PRO HIS CYS PRO ALA ALA LYS ARG VAL VAL GLU GLU SEQRES 3 A 85 VAL ALA ASN GLU MET PRO ASP ALA VAL GLU VAL GLU TYR SEQRES 4 A 85 ILE ASN VAL MET GLU ASN PRO GLN LYS ALA MET GLU TYR SEQRES 5 A 85 GLY ILE MET ALA VAL PRO THR ILE VAL ILE ASN GLY ASP SEQRES 6 A 85 VAL GLU PHE ILE GLY ALA PRO THR LYS GLU ALA LEU VAL SEQRES 7 A 85 GLU ALA ILE LYS LYS ARG LEU HELIX 1 1 ALA A 18 MET A 30 1 13 HELIX 2 2 LYS A 73 LEU A 84 1 12 SHEET 1 A 4 VAL A 34 ASN A 40 0 SHEET 2 A 4 VAL A 3 THR A 9 1 O VAL A 3 N GLU A 35 SHEET 3 A 4 THR A 58 ILE A 61 -1 O THR A 58 N PHE A 8 SHEET 4 A 4 ASP A 64 GLU A 66 -1 N ASP A 64 O ILE A 61 CISPEP 1 VAL A 56 PRO A 57 1 -6.26 CISPEP 2 VAL A 56 PRO A 57 2 -8.23 CISPEP 3 VAL A 56 PRO A 57 3 -12.04 CISPEP 4 VAL A 56 PRO A 57 4 -6.82 CISPEP 5 VAL A 56 PRO A 57 5 -6.82 CISPEP 6 VAL A 56 PRO A 57 6 6.86 CISPEP 7 VAL A 56 PRO A 57 7 0.36 CISPEP 8 VAL A 56 PRO A 57 8 -20.70 CISPEP 9 VAL A 56 PRO A 57 9 1.38 CISPEP 10 VAL A 56 PRO A 57 10 -14.83 CISPEP 11 VAL A 56 PRO A 57 11 -9.62 CISPEP 12 VAL A 56 PRO A 57 12 -14.01 CISPEP 13 VAL A 56 PRO A 57 13 -10.28 CISPEP 14 VAL A 56 PRO A 57 14 -14.99 CISPEP 15 VAL A 56 PRO A 57 15 -4.34 CISPEP 16 VAL A 56 PRO A 57 16 -9.78 CISPEP 17 VAL A 56 PRO A 57 17 -20.71 CISPEP 18 VAL A 56 PRO A 57 18 -4.34 CISPEP 19 VAL A 56 PRO A 57 19 -9.10 CISPEP 20 VAL A 56 PRO A 57 20 -0.64 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