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- PDB-1siw: Crystal structure of the apomolybdo-NarGHI -

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Basic information

Entry
Database: PDB / ID: 1siw
TitleCrystal structure of the apomolybdo-NarGHI
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / apomolybdo-NarGHI / electron-transfer / membrane protein
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
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 / : ...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, 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 / ADC-like domains / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / 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 / Defensin A-like / Barwin-like endoglucanases / N-terminal domain of TfIIb / Aspartate decarboxylase-like domain superfamily / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / FE3-S4 CLUSTER / GUANOSINE-5'-DIPHOSPHATE / PROTOPORPHYRIN IX CONTAINING FE / 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 / CNS refinement / Resolution: 2.2 Å
AuthorsRothery, R.A. / Bertero, M.G. / Cammack, R. / Palak, M. / Blasco, F. / Strynadka, N.C. / Weiner, J.H.
Citation
Journal: Biochemistry / Year: 2004
Title: The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state
Authors: Rothery, R.A. / Bertero, M.G. / Cammack, R. / Palak, M. / Blasco, F. / Strynadka, N.C. / Weiner, J.H.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2003
Title: Insights Into the Respiratory Electron Transfer Pathway from the Structure of Nitrate Reductase A
Authors: Bertero, M.G. / Rothery, R.A. / Palak, M. / Hou, C. / Lim, D. / Blasco, F. / Weiner, J.H. / Strynadka, N.C.J.
History
DepositionMar 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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 1.4Nov 20, 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

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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)229,00813
Polymers224,2193
Non-polymers4,78910
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24740 Å2
ΔGint-230 kcal/mol
Surface area59850 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)458,01626
Polymers448,4396
Non-polymers9,57720
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area63030 Å2
ΔGint-527 kcal/mol
Surface area106140 Å2
MethodPISA
3
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)458,01626
Polymers448,4396
Non-polymers9,57720
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area51140 Å2
ΔGint-478 kcal/mol
Surface area118040 Å2
MethodPISA
4
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)458,01626
Polymers448,4396
Non-polymers9,57720
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 area28730 Å2
ΔGint-415 kcal/mol
Surface area140440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.001, 241.282, 140.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
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 / E.C.1.7.99.4


Mass: 140526.781 Da / Num. of mol.: 1 / Fragment: NarG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Operon narGHJI: NARG, NARC, BISD, B1224 / 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 / E.C.1.7.99.4


Mass: 58140.312 Da / Num. of mol.: 1 / Fragment: NarH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Operon narGHJI: NARH, B1225 / 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 / E.C.1.7.99.4 / 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 (E. coli) / Gene: Operon narGHJI: NARI, CHLI, B1227 / Plasmid: pVA700 / Production host: Escherichia coli (E. coli) / Strain (production host): LCB79 / References: UniProt: P11350, nitrate reductase

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Non-polymers , 6 types, 608 molecules

#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#6: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H77O8P
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#8: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.84 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: peg 3000, hepes, 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
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 131933 / Num. obs: 128499 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 16.4 Å2 / Rsym value: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.351 / % possible all: 85.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: CNS refinement / Resolution: 2.2→29.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5806555.38 / 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
Rfree0.244 6475 5 %RANDOM
Rwork0.203 ---
obs0.203 128499 97.3 %-
all-131933 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4484 Å2 / ksol: 0.324775 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--12.93 Å20 Å2
3----11.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15634 0 198 598 16430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 941 4.9 %
Rwork0.275 18131 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PARGDP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMLIPID.TOP
X-RAY DIFFRACTION4SF_APO.PARSF_APO.TOP
X-RAY DIFFRACTION5HEME.PARHEME.TOP

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