10 20 30 40 50 60 70 80 1YJI - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 14-JAN-05 1YJI
TITLE RDC-REFINED SOLUTION NMR STRUCTURE OF REDUCED PUTIDAREDOXIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTIDAREDOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PDX; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: CAMB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NCM533; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PUC19; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PKM536
KEYWDS FERREDOXIN, [2FE-2S], REDOX, IRON-SULFUR, ELECTRON TRANSFER, KEYWDS 2 NMR, CYTOCHROME P450CAM, ELECTRON TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 11
AUTHOR N.U.JAIN,E.TJIOE,A.SAVIDOR,J.BOULIE
REVDAT 2 24-FEB-09 1YJI 1 VERSN REVDAT 1 28-JUN-05 1YJI 0
JRNL AUTH N.U.JAIN,E.TJIOE,A.SAVIDOR,J.BOULIE JRNL TITL REDOX-DEPENDENT STRUCTURAL DIFFERENCES IN JRNL TITL 2 PUTIDAREDOXIN DERIVED FROM HOMOLOGOUS STRUCTURE JRNL TITL 3 REFINEMENT VIA RESIDUAL DIPOLAR COUPLINGS. JRNL REF BIOCHEMISTRY V. 44 9067 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15966730 JRNL DOI 10.1021/BI050152C
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.C.POCHAPSKY,N.U.JAIN,M.KUTI,T.A.LYONS,J.HEYMONT REMARK 1 TITL A REFINED MODEL FOR THE SOLUTION STRUCTURE OF REMARK 1 TITL 2 OXIDIZED PUTIDAREDOXIN REMARK 1 REF BIOCHEMISTRY V. 38 4681 1999 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 10200155 REMARK 1 DOI 10.1021/BI983030B REMARK 1 REFERENCE 2 REMARK 1 AUTH A.MULLER,J.J.MULLER,Y.A.MULLER,H.UHLMANN, REMARK 1 AUTH 2 R.BERNHARDT,U.HEINEMANN REMARK 1 TITL NEW ASPECTS OF ELECTRON TRANSFER REVEALED BY THE REMARK 1 TITL 2 CRYSTAL STRUCTURE OF A TRUNCATED BOVINE REMARK 1 TITL 3 ADRENODOXIN, ADX(4-108) REMARK 1 REF STRUCTURE V. 6 269 1998 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 9551550 REMARK 1 DOI 10.1016/S0969-2126(98)00031-8 REMARK 1 REFERENCE 3 REMARK 1 AUTH T.C.POCHAPSKY,X.M.YE,G.RATNASWAMY,T.A.LYONS REMARK 1 TITL AN NMR-DERIVED MODEL FOR THE SOLUTION STRUCTURE OF REMARK 1 TITL 2 OXIDIZED PUTIDAREDOXIN, A 2FE-2S FERREDOXIN FROM REMARK 1 TITL 3 PSEUDOMONAS REMARK 1 REF BIOCHEMISTRY V. 33 6424 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 8204575 REMARK 1 DOI 10.1021/BI00187A006 REMARK 1 REFERENCE 4 REMARK 1 AUTH T.C.POCHAPSKY,G.RATNASWAMY,A.PATERA REMARK 1 TITL REDOX-DEPENDENT 1H NMR SPECTRAL FEATURES AND REMARK 1 TITL 2 TERTIARY STRUCTURAL CONSTRAINTS ON THE C-TERMINAL REMARK 1 TITL 3 REGION OF PUTIDAREDOXIN REMARK 1 REF BIOCHEMISTRY V. 33 6433 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 8204576 REMARK 1 DOI 10.1021/BI00187A007
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.9.6 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 1241 NOE REMARK 3 RESTRIANTS, 160 DIHEDRAL ANGLE RESTRAINTS AND 150 RDC REMARK 3 RESTRAINTS, 28 PARAMAGNETIC DISTANCE RESTRAINTS FROM REMARK 3 RELAXATION MEASUREMENTS AND 18 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS
REMARK 4 REMARK 4 1YJI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031583.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 50 MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM REDUCED PUTIDAREDOXIN REMARK 210 15N; 50 MM TRIS-CL BUFFER, 50 REMARK 210 MM KCL, PH 7.4 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-COUPLED 2D 15N-1H HSQC; REMARK 210 7.5% BICELLE (DMPC:DHPC-2.9:1) REMARK 210 , 15N-COUPLED 2D 15N-1H HSQC; REMARK 210 10 MG/ML PHAGE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 9 REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE REFINED AGAINST 15N-1H RDC REMARK 210 RESTRAINTS USING PREVIOUSLY PUBLISHED NOE AND DIHEDRAL ANGLE REMARK 210 RESTRAINTS FOR PDX. THE RESTRAINTS FOR THE METAL BINDING LOOP REMARK 210 (RESIDUES 36-48,85-86) WERE MODELED FROM BOVINE ADRENODOXIN REMARK 210 CRYSTAL STRUCTURE.
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 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 TYR A 33 N ILE A 35 2.17 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 7 -153.63 -79.60 REMARK 500 1 LEU A 15 -164.48 -117.47 REMARK 500 1 ASP A 34 72.96 -38.11 REMARK 500 1 ILE A 35 20.21 -156.04 REMARK 500 1 VAL A 36 171.79 56.76 REMARK 500 1 SER A 42 39.94 -99.04 REMARK 500 1 ALA A 43 77.68 42.34 REMARK 500 1 SER A 44 15.56 -166.63 REMARK 500 1 CYS A 48 46.84 -96.42 REMARK 500 1 GLU A 54 15.26 -58.19 REMARK 500 1 PRO A 61 92.74 -56.23 REMARK 500 1 ASN A 64 -165.38 -59.31 REMARK 500 1 GLU A 72 30.38 -92.26 REMARK 500 1 GLN A 87 39.58 -74.79 REMARK 500 1 LEU A 94 31.39 -90.85 REMARK 500 2 SER A 7 -159.66 -72.30 REMARK 500 2 ASP A 9 5.23 -66.34 REMARK 500 2 MET A 24 -16.28 -49.46 REMARK 500 2 ILE A 32 -52.07 -124.09 REMARK 500 2 ASP A 34 65.59 -106.91 REMARK 500 2 SER A 42 41.65 -99.91 REMARK 500 2 ALA A 43 76.09 43.71 REMARK 500 2 SER A 44 23.54 -166.22 REMARK 500 2 GLU A 54 13.90 -57.38 REMARK 500 2 PRO A 61 94.19 -53.97 REMARK 500 2 ASN A 64 -175.02 -65.18 REMARK 500 2 GLU A 77 105.33 -59.64 REMARK 500 2 SER A 82 165.66 -47.21 REMARK 500 2 GLN A 87 33.80 -79.61 REMARK 500 3 SER A 7 -158.60 -76.51 REMARK 500 3 ASP A 9 2.06 -66.39 REMARK 500 3 TYR A 33 49.32 -40.41 REMARK 500 3 ILE A 35 -177.88 -47.12 REMARK 500 3 VAL A 36 91.48 60.63 REMARK 500 3 CYS A 39 15.70 -69.81 REMARK 500 3 SER A 42 35.12 -93.38 REMARK 500 3 ALA A 43 74.56 45.20 REMARK 500 3 SER A 44 26.44 -166.65 REMARK 500 3 CYS A 48 54.21 -97.28 REMARK 500 3 GLU A 54 9.96 -55.85 REMARK 500 3 PRO A 61 99.33 -58.31 REMARK 500 3 ASN A 64 -178.20 -59.30 REMARK 500 3 ARG A 83 146.28 -171.72 REMARK 500 3 GLN A 87 32.05 -87.53 REMARK 500 4 SER A 7 -160.28 -77.92 REMARK 500 4 LEU A 15 -165.19 -117.88 REMARK 500 4 ASP A 34 54.47 -58.11 REMARK 500 4 ILE A 35 -86.63 -126.91 REMARK 500 4 ASP A 38 -91.93 -87.44 REMARK 500 4 SER A 42 14.12 -155.90 REMARK 500 4 SER A 44 22.21 -162.57 REMARK 500 4 CYS A 45 -156.25 -155.76 REMARK 500 4 ALA A 46 21.38 -149.04 REMARK 500 4 CYS A 48 48.11 -91.37 REMARK 500 4 GLU A 54 12.13 -56.09 REMARK 500 4 PRO A 61 101.96 -48.70 REMARK 500 4 ASN A 64 -175.17 -53.56 REMARK 500 4 GLU A 77 106.80 -58.07 REMARK 500 4 CYS A 86 5.94 -60.65 REMARK 500 4 LEU A 94 32.72 -95.58 REMARK 500 5 SER A 7 -153.28 -82.44 REMARK 500 5 ILE A 32 -63.44 -124.53 REMARK 500 5 VAL A 36 163.40 55.73 REMARK 500 5 ASP A 38 -83.58 -87.73 REMARK 500 5 CYS A 39 15.84 -69.73 REMARK 500 5 SER A 42 22.40 -159.51 REMARK 500 5 SER A 44 23.12 -160.81 REMARK 500 5 GLU A 54 13.99 -57.32 REMARK 500 5 PRO A 61 84.93 -51.33 REMARK 500 5 ALA A 62 105.17 -58.79 REMARK 500 5 ASN A 64 -172.84 -61.61 REMARK 500 5 GLN A 87 49.54 -92.33 REMARK 500 6 SER A 7 -160.08 -72.70 REMARK 500 6 ASP A 9 2.71 -64.94 REMARK 500 6 ASP A 34 74.27 -38.01 REMARK 500 6 ILE A 35 4.61 -150.49 REMARK 500 6 VAL A 36 104.22 56.14 REMARK 500 6 SER A 42 38.07 -94.22 REMARK 500 6 ALA A 43 72.54 44.47 REMARK 500 6 SER A 44 27.70 -166.26 REMARK 500 6 CYS A 48 54.18 -97.70 REMARK 500 6 GLU A 54 8.16 -57.01 REMARK 500 6 ASN A 64 -167.73 -66.37 REMARK 500 6 GLU A 77 104.39 -56.10 REMARK 500 6 GLN A 87 29.57 -75.61 REMARK 500 7 SER A 7 -157.71 -75.38 REMARK 500 7 ASP A 9 1.75 -65.39 REMARK 500 7 LEU A 15 -166.04 -120.28 REMARK 500 7 ILE A 32 -63.71 -122.77 REMARK 500 7 ASP A 34 -37.63 -37.45 REMARK 500 7 ILE A 35 130.70 -19.80 REMARK 500 7 VAL A 36 151.25 -35.56 REMARK 500 7 ASP A 38 -76.53 -88.40 REMARK 500 7 SER A 42 31.00 -160.76 REMARK 500 7 ALA A 43 70.43 50.36 REMARK 500 7 SER A 44 21.16 -165.23 REMARK 500 7 CYS A 48 47.96 -90.77 REMARK 500 7 GLU A 54 10.08 -55.76 REMARK 500 7 PRO A 61 105.00 -59.56 REMARK 500 7 ASN A 64 -169.81 -58.62 REMARK 500 7 GLU A 65 0.35 -65.31 REMARK 500 7 ILE A 68 -19.76 -45.43 REMARK 500 7 GLU A 77 105.28 -53.45 REMARK 500 7 GLN A 87 35.83 -91.56 REMARK 500 7 LEU A 94 35.96 -93.75 REMARK 500 8 SER A 7 -161.48 -75.56 REMARK 500 8 ILE A 32 -57.79 -121.35 REMARK 500 8 VAL A 36 160.32 56.95 REMARK 500 8 ASP A 38 -73.48 -87.67 REMARK 500 8 SER A 42 36.07 -93.90 REMARK 500 8 ALA A 43 72.47 43.20 REMARK 500 8 SER A 44 17.42 -163.97 REMARK 500 8 GLU A 54 11.57 -54.16 REMARK 500 8 PRO A 61 105.38 -55.57 REMARK 500 8 ASN A 64 -171.30 -61.81 REMARK 500 8 GLU A 65 1.49 -69.41 REMARK 500 8 SER A 82 172.10 -55.41 REMARK 500 8 GLN A 87 37.86 -94.48 REMARK 500 9 SER A 7 -163.65 -74.54 REMARK 500 9 LEU A 15 -164.70 -119.06 REMARK 500 9 ASP A 34 67.01 -103.58 REMARK 500 9 SER A 42 40.60 -98.55 REMARK 500 9 ALA A 43 75.79 42.98 REMARK 500 9 SER A 44 26.01 -166.54 REMARK 500 9 CYS A 48 53.91 -92.74 REMARK 500 9 GLU A 54 14.13 -56.67 REMARK 500 9 PRO A 61 90.52 -55.31 REMARK 500 9 ASN A 64 -172.10 -60.74 REMARK 500 9 GLU A 77 106.14 -59.76 REMARK 500 9 GLN A 87 42.83 -81.29 REMARK 500 10 SER A 7 -159.92 -72.15 REMARK 500 10 LEU A 15 -165.29 -119.40 REMARK 500 10 ILE A 32 -60.30 -124.51 REMARK 500 10 VAL A 36 159.48 57.46 REMARK 500 10 ASP A 38 -85.42 -88.42 REMARK 500 10 CYS A 39 10.36 -65.76 REMARK 500 10 SER A 42 28.55 -160.30 REMARK 500 10 SER A 44 17.16 -159.15 REMARK 500 10 GLU A 54 14.60 -56.36 REMARK 500 10 PRO A 61 97.68 -59.43 REMARK 500 10 ALA A 63 152.17 -47.03 REMARK 500 10 ASN A 64 -169.81 -61.10 REMARK 500 10 GLU A 77 102.66 -59.00 REMARK 500 10 GLN A 87 33.04 -91.18 REMARK 500 11 SER A 7 -155.83 -73.73 REMARK 500 11 ASP A 9 2.07 -66.03 REMARK 500 11 LEU A 15 -165.54 -117.79 REMARK 500 11 TYR A 33 49.28 -48.10 REMARK 500 11 ILE A 35 -167.02 -54.02 REMARK 500 11 VAL A 36 99.88 58.84 REMARK 500 11 SER A 42 35.98 -93.77 REMARK 500 11 ALA A 43 70.58 44.72 REMARK 500 11 SER A 44 26.60 -163.47 REMARK 500 11 CYS A 45 -159.44 -158.90 REMARK 500 11 GLU A 54 9.15 -56.35 REMARK 500 11 PRO A 61 102.74 -49.47 REMARK 500 11 LEU A 94 31.04 -98.10 REMARK 500 REMARK 500 REMARK: NULL
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 1 FES A 107 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 CYS A 45 SG 125.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 FES A 107 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 48 SG REMARK 620 2 CYS A 86 SG 120.7 REMARK 620 N 1
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 107
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PDX RELATED DB: PDB REMARK 900 RELATED ID: 4154 RELATED DB: BMRB REMARK 900 RELATED ID: 1YJJ RELATED DB: PDB
DBREF 1YJI A 1 106 UNP P00259 PUTX_PSEPU 1 106
SEQRES 1 A 106 SER LYS VAL VAL TYR VAL SER HIS ASP GLY THR ARG ARG SEQRES 2 A 106 GLU LEU ASP VAL ALA ASP GLY VAL SER LEU MET GLN ALA SEQRES 3 A 106 ALA VAL SER ASN GLY ILE TYR ASP ILE VAL GLY ASP CYS SEQRES 4 A 106 GLY GLY SER ALA SER CYS ALA THR CYS HIS VAL TYR VAL SEQRES 5 A 106 ASN GLU ALA PHE THR ASP LYS VAL PRO ALA ALA ASN GLU SEQRES 6 A 106 ARG GLU ILE GLY MET LEU GLU CYS VAL THR ALA GLU LEU SEQRES 7 A 106 LYS PRO ASN SER ARG LEU CYS CYS GLN ILE ILE MET THR SEQRES 8 A 106 PRO GLU LEU ASP GLY ILE VAL VAL ASP VAL PRO ASP ARG SEQRES 9 A 106 GLN TRP
HET FES A 107 4
HETNAM FES FE2/S2 (INORGANIC) CLUSTER
FORMUL 2 FES FE2 S2
HELIX 1 1 SER A 22 ASN A 30 1 9 HELIX 2 2 ASN A 64 LEU A 71 1 8 HELIX 3 3 GLU A 72 VAL A 74 5 3 HELIX 4 4 CYS A 86 ILE A 88 5 3 HELIX 5 5 THR A 91 ASP A 95 5 5
SHEET 1 A 5 ARG A 12 ASP A 16 0 SHEET 2 A 5 LYS A 2 VAL A 6 -1 N VAL A 3 O LEU A 15 SHEET 3 A 5 ILE A 97 ASP A 100 1 O VAL A 99 N VAL A 6 SHEET 4 A 5 HIS A 49 VAL A 52 -1 N TYR A 51 O ASP A 100 SHEET 5 A 5 SER A 82 LEU A 84 -1 O ARG A 83 N VAL A 50
LINK SG CYS A 39 FE1 FES A 107 1555 1555 2.20 LINK SG CYS A 45 FE1 FES A 107 1555 1555 2.20 LINK SG CYS A 48 FE2 FES A 107 1555 1555 2.19 LINK SG CYS A 86 FE2 FES A 107 1555 1555 2.18
SITE 1 AC1 7 MET A 24 CYS A 39 SER A 44 CYS A 45 SITE 2 AC1 7 CYS A 48 LEU A 84 CYS A 86
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