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- PDB-3egw: The crystal structure of the NarGHI mutant NarH - C16A -

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Basic information

Entry
Database: PDB / ID: 3egw
TitleThe crystal structure of the NarGHI mutant NarH - C16A
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / nitrate reduction / 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
Rossmann fold - #12440 / 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 ...Rossmann fold - #12440 / 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 / 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 / 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 / Few Secondary Structures / Irregular / Alpha-Beta Plaits / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / 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 / Chem-MGD / 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 / Resolution: 1.9 Å
AuthorsBertero, M.G. / Rothery, R.A. / Weiner, J.H. / Strynadka, N.C.J.
CitationJournal: To be Published
Title: When width is more important than height: Barriers to electron transfer in E.coli nitrate reductase
Authors: Parkin, A. / Blanford, C.F. / Rothery, R.A. / Macey, R. / Bertero, M. / Strynadka, N.C.J. / Armstrong, F.A. / Weiner, J.H.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 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
Revision 1.4Aug 30, 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)228,97315
Polymers223,3563
Non-polymers5,61712
Water27,4911526
1
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)457,94730
Polymers446,7136
Non-polymers11,23424
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area49470 Å2
ΔGint-188 kcal/mol
Surface area109350 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18130 Å2
ΔGint-61 kcal/mol
Surface area61280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.995, 241.684, 139.475
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 alpha subunit


Mass: 140178.375 Da / Num. of mol.: 1 / Fragment: Chain A, NarG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narG, bisD, narC, b1224, JW1215 / 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 / Nitrate reductase A subunit beta / Quinol-nitrate oxidoreductase subunit beta


Mass: 57775.863 Da / Num. of mol.: 1 / Fragment: Chain B, NarH / Mutation: C16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narH, b1225, JW1216 / 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 / Nitrate reductase A subunit gamma / Quinol-nitrate oxidoreductase gamma subunit / Cytochrome B-NR


Mass: 25402.221 Da / Num. of mol.: 1 / Fragment: Chain C, NarI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narI, chlI, b1227, JW1218 / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11350, nitrate reductase

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Non-polymers , 9 types, 1538 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.: 1 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#8: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


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


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


Mass: 18.015 Da / Num. of mol.: 1526 / 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: 2.91 Å3/Da / Density % sol: 57.66 %
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

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 195446 / % possible obs: 96.2 % / Rmerge(I) obs: 0.057 / Χ2: 1.06 / Net I/σ(I): 21.771
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.252 / Num. unique all: 15338 / Χ2: 1.081 / % possible all: 76.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CNSphasing
CNS1.1refinement
RefinementStarting model: 1Q16

1q16


Resolution: 1.9→19.99 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 5799808 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 9737 5 %RANDOM
Rwork0.175 ---
obs-195208 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.684 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 58.4 Å2 / Biso mean: 20.863 Å2 / Biso min: 4.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å20 Å2
2--8.37 Å20 Å2
3----7.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15711 0 267 1526 17504
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 1322 4.8 %
Rwork0.221 25997 -
all-27319 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cofact.parcofact.top
X-RAY DIFFRACTION3water_rep.paramlipid.top
X-RAY DIFFRACTION4sf.parsf.top
X-RAY DIFFRACTION5heme.parheme.top

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