HEADER OXIDOREDUCTASE 03-OCT-07 2RM5 TITLE GLUTATHIONE PEROXIDASE-TYPE TRYPAREDOXIN PEROXIDASE, OXIDIZED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE PEROXIDASE-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 10-176; COMPND 5 SYNONYM: TRYPANOTHIONE/TRYPAREDOXIN DEPENDENT PEROXIDASE 3; COMPND 6 EC: 1.11.1.9; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: GPX3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRYPAREDOXIN, PEROXIDASE, OXIDIZED, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.MELCHERS,K.FEHER,M.DIECHTIEROW,L.KRAUTH-SIEGEL,I.TEWS,C.MUHLE-GOLL REVDAT 5 30-OCT-24 2RM5 1 REMARK REVDAT 4 10-NOV-21 2RM5 1 REMARK SEQADV REVDAT 3 16-OCT-13 2RM5 1 JRNL VERSN REVDAT 2 24-FEB-09 2RM5 1 VERSN REVDAT 1 29-JUL-08 2RM5 0 JRNL AUTH J.MELCHERS,M.DIECHTIEROW,K.FEHER,I.SINNING,I.TEWS, JRNL AUTH 2 R.L.KRAUTH-SIEGEL,C.MUHLE-GOLL JRNL TITL STRUCTURAL BASIS FOR A DISTINCT CATALYTIC MECHANISM IN JRNL TITL 2 TRYPANOSOMA BRUCEI TRYPAREDOXIN PEROXIDASE JRNL REF J.BIOL.CHEM. V. 283 30401 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18684708 JRNL DOI 10.1074/JBC.M803563200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RM5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000150024. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 297 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2MM [U-100% 15N] TRYPAREDOXIN REMARK 210 PEROXIDASE; 90% H2O/10% D2O; REMARK 210 1.2MM [U-100% 13C; U-100% 15N] REMARK 210 TRYPAREDOXIN PEROXIDASE; 100% REMARK 210 D2O; 1.2 MM TRYPAREDOXIN REMARK 210 PEROXIDASE; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 HD1 TYR A 61 H VAL A 71 1.19 REMARK 500 HD1 HIS A 116 HB3 LEU A 118 1.27 REMARK 500 HB2 LEU A 143 HE1 PHE A 154 1.27 REMARK 500 HG3 PRO A 84 HG21 ILE A 135 1.27 REMARK 500 HG23 ILE A 135 HZ3 TRP A 137 1.30 REMARK 500 HB2 PRO A 75 HB3 LYS A 107 1.31 REMARK 500 HZ PHE A 98 HZ PHE A 102 1.31 REMARK 500 HD1 PHE A 16 HG LEU A 30 1.32 REMARK 500 HB2 SER A 45 HB3 PRO A 75 1.32 REMARK 500 HG2 PRO A 37 HA LEU A 171 1.33 REMARK 500 HB3 LEU A 21 HA HIS A 25 1.33 REMARK 500 OE1 GLU A 120 HZ3 LYS A 123 1.56 REMARK 500 O ALA A 131 HG1 THR A 132 1.57 REMARK 500 OE2 GLU A 152 HZ3 LYS A 166 1.60 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 3 TYR A 119 CE1 TYR A 119 CZ -0.088 REMARK 500 3 TYR A 119 CZ TYR A 119 CE2 0.080 REMARK 500 4 PHE A 98 CE1 PHE A 98 CZ 0.146 REMARK 500 4 PHE A 98 CZ PHE A 98 CE2 -0.124 REMARK 500 4 PHE A 142 CE1 PHE A 142 CZ 0.128 REMARK 500 5 PHE A 142 CE1 PHE A 142 CZ 0.128 REMARK 500 7 PHE A 98 CE1 PHE A 98 CZ 0.117 REMARK 500 7 PHE A 142 CE1 PHE A 142 CZ 0.141 REMARK 500 9 PHE A 98 CZ PHE A 98 CE2 0.122 REMARK 500 11 PHE A 74 CE1 PHE A 74 CZ 0.141 REMARK 500 12 PHE A 74 CE1 PHE A 74 CZ 0.120 REMARK 500 14 PHE A 74 CE1 PHE A 74 CZ 0.121 REMARK 500 15 PHE A 142 CE1 PHE A 142 CZ 0.168 REMARK 500 15 PHE A 142 CZ PHE A 142 CE2 -0.126 REMARK 500 16 PHE A 74 CE1 PHE A 74 CZ 0.135 REMARK 500 17 PHE A 74 CE1 PHE A 74 CZ 0.135 REMARK 500 18 PHE A 74 CE1 PHE A 74 CZ 0.124 REMARK 500 18 PHE A 142 CE1 PHE A 142 CZ 0.130 REMARK 500 20 PHE A 74 CE1 PHE A 74 CZ 0.126 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 51 44.12 -77.51 REMARK 500 1 PRO A 84 -117.46 -12.25 REMARK 500 1 ILE A 90 35.28 -78.55 REMARK 500 1 LYS A 97 97.26 13.27 REMARK 500 1 LYS A 99 150.07 66.94 REMARK 500 1 ALA A 100 -165.65 -171.29 REMARK 500 1 MET A 105 -162.26 -103.24 REMARK 500 1 ASN A 111 -178.88 171.84 REMARK 500 1 THR A 132 -172.46 58.96 REMARK 500 1 ASN A 138 -161.25 -46.66 REMARK 500 1 THR A 140 94.49 37.78 REMARK 500 1 SER A 155 -178.65 -67.50 REMARK 500 1 PRO A 156 10.99 -63.92 REMARK 500 1 ARG A 175 -67.63 -120.02 REMARK 500 2 ASP A 22 -176.43 -68.53 REMARK 500 2 ASN A 29 85.44 -69.90 REMARK 500 2 LYS A 46 31.97 76.18 REMARK 500 2 THR A 50 -38.67 -137.24 REMARK 500 2 LYS A 51 -12.88 69.47 REMARK 500 2 PRO A 84 -105.12 -27.71 REMARK 500 2 ASN A 86 58.58 -114.58 REMARK 500 2 LYS A 97 77.58 33.36 REMARK 500 2 ALA A 100 -162.22 -125.11 REMARK 500 2 MET A 105 -151.26 -110.79 REMARK 500 2 ASN A 111 179.23 171.93 REMARK 500 2 LYS A 133 -9.76 69.58 REMARK 500 2 ASN A 138 -158.39 -47.90 REMARK 500 2 THR A 140 104.68 48.51 REMARK 500 2 SER A 173 121.96 -170.48 REMARK 500 2 ARG A 175 -42.53 -177.67 REMARK 500 3 HIS A 25 25.27 83.74 REMARK 500 3 ASN A 29 84.12 -67.84 REMARK 500 3 PRO A 84 -155.60 -71.37 REMARK 500 3 ASN A 86 92.24 66.26 REMARK 500 3 ILE A 90 43.15 -80.89 REMARK 500 3 LYS A 97 111.12 -38.97 REMARK 500 3 LYS A 99 146.60 66.66 REMARK 500 3 ALA A 100 -165.87 -166.63 REMARK 500 3 MET A 105 -150.44 -115.37 REMARK 500 3 ASN A 111 179.41 170.52 REMARK 500 3 LYS A 133 -60.08 177.05 REMARK 500 3 LYS A 136 -35.82 179.02 REMARK 500 3 ASN A 138 -157.32 -44.46 REMARK 500 3 PHE A 139 -56.96 -28.56 REMARK 500 3 THR A 140 95.73 42.87 REMARK 500 3 PRO A 150 99.87 -66.90 REMARK 500 3 SER A 173 126.49 -171.58 REMARK 500 3 ARG A 175 -29.44 177.71 REMARK 500 4 SER A 13 -54.44 72.46 REMARK 500 4 ASN A 29 93.85 -66.73 REMARK 500 REMARK 500 THIS ENTRY HAS 365 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 CYS A 95 THR A 96 13 -140.83 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 PHE A 142 0.06 SIDE CHAIN REMARK 500 5 TYR A 64 0.06 SIDE CHAIN REMARK 500 6 TYR A 64 0.06 SIDE CHAIN REMARK 500 7 PHE A 142 0.06 SIDE CHAIN REMARK 500 9 TYR A 64 0.05 SIDE CHAIN REMARK 500 10 TYR A 119 0.06 SIDE CHAIN REMARK 500 12 TYR A 64 0.06 SIDE CHAIN REMARK 500 15 TYR A 64 0.06 SIDE CHAIN REMARK 500 16 TYR A 64 0.07 SIDE CHAIN REMARK 500 17 TYR A 61 0.07 SIDE CHAIN REMARK 500 17 TYR A 64 0.05 SIDE CHAIN REMARK 500 20 TYR A 64 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RM6 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHOR STATES THAT THE SEQUENCE DIFFERS FROM THE SEQUENCE REMARK 999 DEPOSITED IN THE NCBI BECAUSE OF MICRO HETEROGENICITY IN THE REMARK 999 PEROXIDASE GENE. DBREF 2RM5 A 13 176 UNP Q869A5 Q869A5_9TRYP 13 176 SEQADV 2RM5 GLY A 10 UNP Q869A5 EXPRESSION TAG SEQADV 2RM5 MET A 11 UNP Q869A5 EXPRESSION TAG SEQADV 2RM5 GLY A 12 UNP Q869A5 EXPRESSION TAG SEQADV 2RM5 THR A 59 UNP Q869A5 ALA 59 SEE REMARK 999 SEQADV 2RM5 SER A 76 UNP Q869A5 CYS 76 ENGINEERED MUTATION SEQADV 2RM5 ASN A 86 UNP Q869A5 THR 86 SEE REMARK 999 SEQRES 1 A 167 GLY MET GLY SER SER ILE PHE ASP PHE GLU VAL LEU ASP SEQRES 2 A 167 ALA ASP HIS LYS PRO TYR ASN LEU VAL GLN HIS LYS GLY SEQRES 3 A 167 SER PRO LEU LEU ILE TYR ASN VAL ALA SER LYS CYS GLY SEQRES 4 A 167 TYR THR LYS GLY GLY TYR GLU THR ALA THR THR LEU TYR SEQRES 5 A 167 ASN LYS TYR LYS SER GLN GLY PHE THR VAL LEU ALA PHE SEQRES 6 A 167 PRO SER ASN GLN PHE GLY GLY GLN GLU PRO GLY ASN GLU SEQRES 7 A 167 GLU GLU ILE LYS GLU PHE VAL CYS THR LYS PHE LYS ALA SEQRES 8 A 167 GLU PHE PRO ILE MET ALA LYS ILE ASN VAL ASN GLY GLU SEQRES 9 A 167 ASN ALA HIS PRO LEU TYR GLU TYR MET LYS LYS THR LYS SEQRES 10 A 167 PRO GLY ILE LEU ALA THR LYS ALA ILE LYS TRP ASN PHE SEQRES 11 A 167 THR SER PHE LEU ILE ASP ARG ASP GLY VAL PRO VAL GLU SEQRES 12 A 167 ARG PHE SER PRO GLY ALA SER VAL LYS ASP ILE GLU GLU SEQRES 13 A 167 LYS LEU ILE PRO LEU LEU GLY SER ALA ARG LEU HELIX 1 1 SER A 14 PHE A 18 5 5 HELIX 2 2 ASN A 29 LYS A 34 5 6 HELIX 3 3 GLY A 52 LYS A 65 1 14 HELIX 4 4 GLY A 85 GLU A 89 5 5 HELIX 5 5 HIS A 116 LYS A 126 1 11 HELIX 6 6 SER A 159 SER A 173 1 15 SHEET 1 A 2 VAL A 20 LEU A 21 0 SHEET 2 A 2 PRO A 27 TYR A 28 -1 O TYR A 28 N VAL A 20 SHEET 1 B 4 THR A 70 PRO A 75 0 SHEET 2 B 4 LEU A 38 VAL A 43 1 N LEU A 39 O LEU A 72 SHEET 3 B 4 SER A 141 ILE A 144 -1 O ILE A 144 N LEU A 38 SHEET 4 B 4 PRO A 150 PHE A 154 -1 O VAL A 151 N LEU A 143 SSBOND 1 CYS A 47 CYS A 95 1555 1555 2.03 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