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- PDB-1y4z: The crystal structure of Nitrate Reductase A, NarGHI, in complex ... -

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Basic information

Entry
Database: PDB / ID: 1y4z
TitleThe crystal structure of Nitrate Reductase A, NarGHI, in complex with the Q-site inhibitor pentachlorophenol
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / nitrate reduction / electron transfer / membrane protein / Q-site
Function / homology
Function and homology information


nitrate reductase (quinone) / NarGHI complex / nitrate reductase (quinone) activity / nitrate metabolic process / nitrate reductase complex / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...nitrate reductase (quinone) / NarGHI complex / nitrate reductase (quinone) activity / nitrate metabolic process / nitrate reductase complex / nitrate reductase activity / anaerobic electron transport chain / molybdopterin cofactor binding / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Nitrate reductase alpha subunit / Nitrate reductase, gamma subunit / NarG-like domain / NarG-like superfamily / : / Nitrate reductase gamma subunit / nitrate reductase domain fold / nitrate reductase domain like / Nitrate reductase, beta subunit / Respiratory nitrate reductase beta, C-terminal ...Nitrate reductase alpha subunit / Nitrate reductase, gamma subunit / NarG-like domain / NarG-like superfamily / : / Nitrate reductase gamma subunit / nitrate reductase domain fold / nitrate reductase domain like / Nitrate reductase, beta subunit / Respiratory nitrate reductase beta, C-terminal / Nitrate reductase beta, C-terminal domain superfamily / Respiratory nitrate reductase beta C-terminal / Nitrate reductase, alpha subunit / Nitrate reductase, alpha subunit, N-terminal / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Respiratory nitrate reductase alpha N-terminal / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Nitrate reductase alpha subunit-like, MopB domain / Prokaryotic molybdopterin oxidoreductases signature 2. / 4Fe-4S dicluster domain / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / : / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Up-down Bundle / Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chem-AGA / FE3-S4 CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-MD1 / PENTACHLOROPHENOL / IRON/SULFUR CLUSTER / Respiratory nitrate reductase 1 alpha chain / Respiratory nitrate reductase 1 beta chain / Respiratory nitrate reductase 1 gamma chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBertero, M.G. / Rothery, R.A. / Boroumand, N. / Palak, M. / Blasco, F. / Ginet, N. / Weiner, J.H. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and Biochemical Characterization of a Quinol Binding Site of Escherichia coli Nitrate Reductase A
Authors: Bertero, M.G. / Rothery, R.A. / Boroumand, N. / Palak, M. / Blasco, F. / Ginet, N. / Weiner, J.H. / Strynadka, N.C.J.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
C: Respiratory nitrate reductase 1 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,36615
Polymers224,1873
Non-polymers5,17812
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26940 Å2
ΔGint-277 kcal/mol
Surface area58540 Å2
MethodPISA
2
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
C: Respiratory nitrate reductase 1 gamma chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
C: Respiratory nitrate reductase 1 gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)458,73130
Polymers448,3756
Non-polymers10,35724
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area67150 Å2
ΔGint-619 kcal/mol
Surface area103800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.456, 241.342, 140.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-1850-

HOH

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Components

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Respiratory nitrate reductase 1 ... , 3 types, 3 molecules ABC

#1: Protein Respiratory nitrate reductase 1 alpha chain / NarG / Nitrate reductase A alpha subunit / Quinol-nitrate oxidoreductase alpha subunit


Mass: 140526.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narG / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P09152, nitrate reductase
#2: Protein Respiratory nitrate reductase 1 beta chain / NarH / Nitrate reductase A beta subunit / Quinol-nitrate oxidoreductase beta subunit


Mass: 58108.250 Da / Num. of mol.: 1 / Mutation: C26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narH / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11349, nitrate reductase
#3: Protein Respiratory nitrate reductase 1 gamma chain / NarI / Nitrate reductase A gamma subunit / Quinol-nitrate oxidoreductase gamma subunit / Cytochrome B-NR


Mass: 25552.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narI / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11350, nitrate reductase

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Non-polymers , 8 types, 1032 molecules

#4: Chemical ChemComp-MD1 / PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-AGA / (1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE / PHOSPHATIDYL GLYCEROL


Mass: 455.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H36O10P
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-PCI / PENTACHLOROPHENOL


Mass: 266.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6HCl5O
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: peg 3000, sodium acetate, potassium chloride, EDTA, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 28, 2003 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 161680 / Num. obs: 161680 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 12 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 10437 / Rsym value: 0.392 / % possible all: 60

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.75 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6212061.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 9703 6 %RANDOM
Rwork0.188 ---
obs0.188 161410 91.9 %-
all-16141 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5876 Å2 / ksol: 0.336248 e/Å3
Displacement parametersBiso mean: 27.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2--13.57 Å20 Å2
3----10.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15643 0 256 1020 16919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it2.812
X-RAY DIFFRACTIONc_scangle_it3.672.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 1141 6 %
Rwork0.266 18027 -
obs--66.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COFACT.PARAMCOFACT.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4SF.PARAMLIPID1.TOP
X-RAY DIFFRACTION5PCL.PARAMPCL.TOP

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