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- PDB-1y5i: The crystal structure of the NarGHI mutant NarI-K86A -

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Basic information

Entry
Database: PDB / ID: 1y5i
TitleThe crystal structure of the NarGHI mutant NarI-K86A
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / nitrate reduction / membrane protein / electron transfer / Q-site
Function / homology
Function and homology information


nitrate reductase (quinone) / NarGHI complex / nitrate reductase complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / nitrate assimilation ...nitrate reductase (quinone) / NarGHI complex / nitrate reductase complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / membrane / metal ion binding / 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, alpha subunit / Nitrate reductase, beta subunit / Nitrate reductase, alpha subunit, N-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, alpha subunit / Nitrate reductase, beta subunit / Nitrate reductase, alpha subunit, N-terminal / Respiratory nitrate reductase beta, C-terminal / Nitrate reductase beta, C-terminal domain superfamily / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Respiratory nitrate reductase alpha N-terminal / Respiratory nitrate reductase beta C-terminal / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Prokaryotic molybdopterin oxidoreductases signature 2. / 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 / Alpha-Beta Plaits - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / : / Chem-AGA / FE3-S4 CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-MD1 / 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: 1.9 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 2, 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 2.0Sep 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / database_PDB_caveat ...atom_site / database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 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 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)229,83415
Polymers224,1613
Non-polymers5,67312
Water20,1411118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26630 Å2
ΔGint-259 kcal/mol
Surface area58710 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)459,66830
Polymers448,3236
Non-polymers11,34624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area66950 Å2
ΔGint-587 kcal/mol
Surface area103730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.587, 242.399, 139.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 58140.312 Da / Num. of mol.: 1
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: 25494.252 Da / Num. of mol.: 1 / Mutation: K86A
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, 1130 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 / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: 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
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O

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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: 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: 1.9→30 Å / Num. all: 195380 / Num. obs: 195380 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.424 / % possible all: 76.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q16

1q16


Resolution: 1.9→29.74 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5731731.12 / 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
Rfree0.208 9740 5 %RANDOM
Rwork0.176 ---
obs0.176 195315 96.1 %-
all-195315 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7641 Å2 / ksol: 0.347425 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--6.42 Å20 Å2
3----6.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15638 0 263 1118 17019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.112
X-RAY DIFFRACTIONc_scbond_it2.612
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 1202 4.7 %
Rwork0.245 24284 -
obs--75.2 %
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 DIFFRACTION5LIPID2.PARAMLIPID2.TOP

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