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- PDB-1q16: Crystal structure of Nitrate Reductase A, NarGHI, from Escherichi... -

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Basic information

Entry
Database: PDB / ID: 1q16
TitleCrystal structure of Nitrate Reductase A, NarGHI, from Escherichia coli
Components(Respiratory nitrate reductase 1 ...) x 3
KeywordsOXIDOREDUCTASE / membrane protein / electron-transfer
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
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 / MIRAS / Resolution: 1.9 Å
AuthorsBertero, M.G. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.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
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)230,02315
Polymers224,3513
Non-polymers5,67312
Water21,8521213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26790 Å2
ΔGint-251 kcal/mol
Surface area59230 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)460,04730
Polymers448,7016
Non-polymers11,34624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_354-x-2,y,-z-1/21
Buried area67190 Å2
ΔGint-571 kcal/mol
Surface area104850 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)460,04730
Polymers448,7016
Non-polymers11,34624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area55280 Å2
ΔGint-519 kcal/mol
Surface area116750 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)460,04730
Polymers448,7016
Non-polymers11,34624
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 area32990 Å2
ΔGint-468 kcal/mol
Surface area139040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.175, 241.376, 139.494
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
11A-1926-

HOH

21C-868-

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


Mass: 140657.969 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) / References: UniProt: P09152, nitrate reductase
#2: Protein Respiratory nitrate reductase 1 beta chain


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) / References: UniProt: P11349, nitrate reductase
#3: Protein Respiratory nitrate reductase 1 gamma chain / 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) / References: UniProt: P11350, nitrate reductase

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Non-polymers , 8 types, 1225 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-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-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1213 / 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: 57.45 %
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
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES1reservoirpH7.0
220 %(w/v)PEG30001reservoir
3200 mMsodium acetate1reservoir
4200 mM1reservoirKCl
55 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2002
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 202288 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 10 Å2 / Rsym value: 0.081 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 203816 / % possible obs: 99.6 % / Num. measured all: 1267890 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.502

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
SOLVEphasing
SHARPphasing
RESOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→29.68 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 7975224.84 / Data cutoff high rms absF: 7975224.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 10078 5 %RANDOM
Rwork0.202 ---
all0.203 ---
obs0.202 202287 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.9332 Å2 / ksol: 0.336417 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20 Å2
2--10.6 Å20 Å2
3----9.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15718 0 268 1213 17199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.9→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 198 5.1 %
Rwork0.297 4003 -
obs--99.9 %
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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