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- PDB-3ir7: Crystal structure of NarGHI mutant NarG-R94S -

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Basic information

Entry
Database: PDB / ID: 3ir7
TitleCrystal structure of NarGHI mutant NarG-R94S
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / Nitrate reductase / electron transfer / membrane protein / 4Fe-4S / Cell membrane / Electron transport / Iron / Iron-sulfur / Membrane / Metal-binding / Molybdenum / Nitrate assimilation / Transport / 3Fe-4S / Cell inner membrane / Formylation / Heme / Transmembrane
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
AF1104-like - #20 / Defensin A-like - #200 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / AF1104-like / nitrate reductase tail / nitrate reductase tail / Nitrate reductase, gamma subunit / NarG-like domain / NarG-like superfamily / Nitrate reductase gamma subunit ...AF1104-like - #20 / Defensin A-like - #200 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / AF1104-like / nitrate reductase tail / nitrate reductase tail / 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 / ADC-like domains / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 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 / Defensin A-like / N-terminal domain of TfIIb / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helix non-globular / Special / Few Secondary Structures / Irregular / 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 / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBertero, M.G. / Rothery, R.A. / Weiner, J.H. / Strynadka, N.C.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Protein crystallography reveals a role for the FS0 cluster of Escherichia coli nitrate reductase A (NarGHI) in enzyme maturation.
Authors: Rothery, R.A. / Bertero, M.G. / Spreter, T. / Bouromand, N. / Strynadka, N.C. / Weiner, J.H.
History
DepositionAug 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)229,24814
Polymers224,2813
Non-polymers4,96811
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18010 Å2
ΔGint-62 kcal/mol
Surface area61580 Å2
MethodPISA
2
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)229,24814
Polymers224,2813
Non-polymers4,96811
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_354-x-2,y,-z-1/21
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-24 kcal/mol
Surface area74720 Å2
MethodPISA
3
A: Respiratory nitrate reductase 1 alpha chain
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)229,24814
Polymers224,2813
Non-polymers4,96811
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation3_354-x-2,y,-z-1/21
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-34 kcal/mol
Surface area72370 Å2
MethodPISA
4
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)458,49728
Polymers448,5616
Non-polymers9,93622
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area49370 Å2
ΔGint-185 kcal/mol
Surface area109790 Å2
MethodPISA
5
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)458,49728
Polymers448,5616
Non-polymers9,93622
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area37750 Å2
ΔGint-140 kcal/mol
Surface area121410 Å2
MethodPISA
6
A: Respiratory nitrate reductase 1 alpha chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)458,49728
Polymers448,5616
Non-polymers9,93622
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation2_355-x-2,-y,z+1/21
crystal symmetry operation3_354-x-2,y,-z-1/21
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area16170 Å2
ΔGint-83 kcal/mol
Surface area143000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.851, 241.147, 139.966
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 / Nitrate reductase A subunit alpha / Quinol-nitrate oxidoreductase subunit alpha


Mass: 140587.859 Da / Num. of mol.: 1 / Fragment: NarG / Mutation: R95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: narG, bisD, narC, b1224, JW1215 / Production host: Escherichia coli (E. coli) / References: UniProt: P09152, nitrate reductase
#2: Protein Respiratory nitrate reductase 1 beta chain / Nitrate reductase A subunit beta / Quinol-nitrate oxidoreductase subunit beta


Mass: 58140.312 Da / Num. of mol.: 1 / Fragment: NarH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: narH, b1225, JW1216 / Production host: Escherichia coli (E. coli) / References: UniProt: P11349, nitrate reductase
#3: Protein Respiratory nitrate reductase 1 gamma chain / Nitrate reductase A subunit gamma / Quinol-nitrate oxidoreductase subunit gamma / Cytochrome B-NR


Mass: 25552.355 Da / Num. of mol.: 1 / Fragment: NarI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: narI, chlI, b1227, JW1218 / Production host: Escherichia coli (E. coli) / References: UniProt: P11350, nitrate reductase

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Non-polymers , 7 types, 187 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-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#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 / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 3000, sodium acetate, potassium chloride, EDTA, hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 89737 / % possible obs: 99.8 %

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→24.96 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 4320266 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 7209 8 %RANDOM
Rwork0.202 ---
obs-89737 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.124 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso max: 91.27 Å2 / Biso mean: 36.73 Å2 / Biso min: 14.49 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2--15.76 Å20 Å2
3----12.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15681 0 245 176 16102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 1143 7.7 %
Rwork0.269 13683 -
all-14826 -
obs--99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cofact.parcofact.top
X-RAY DIFFRACTION3water_rep.paramlipid1.top
X-RAY DIFFRACTION4sf.parsf.top
X-RAY DIFFRACTION5heme.parheme.top

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