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- PDB-1kqg: FORMATE DEHYDROGENASE N FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1kqg
TitleFORMATE DEHYDROGENASE N FROM E. COLI
Components(FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, ...) x 3
KeywordsOXIDOREDUCTASE / SELENIUM / SELENOCYSTEINE / SECYS / MOLYBDENUM / MOLYBDOPTERIN / MPT / MOLYBDOPTERIN GUANINE DINUCLEOTIDE / MGD / IRON SULFUR CLUSTER / FE4S4 / FORMATE / DEHYDROGENASE / ANAEROBIC / INTEGRAL MEMBRANE PROTEIN
Function / homology
Function and homology information


formate dehydrogenase-N / formate dehydrogenase (quinone) activity / formate oxidation / formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase complex / selenium binding / anaerobic electron transport chain / heme oxidation / formate dehydrogenase (NAD+) activity / molybdenum ion binding ...formate dehydrogenase-N / formate dehydrogenase (quinone) activity / formate oxidation / formate dehydrogenase (cytochrome-c-553) activity / formate dehydrogenase complex / selenium binding / anaerobic electron transport chain / heme oxidation / formate dehydrogenase (NAD+) activity / molybdenum ion binding / anaerobic respiration / molybdopterin cofactor binding / respiratory electron transport chain / outer membrane-bounded periplasmic space / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Single helix bin / Formate dehydrogenase iron-sulphur subunit, Proteobacteria / Formate dehydrogenase, gamma subunit / Formate dehydrogenase iron-sulphur subunit / Formate dehydrogenase, transmembrane / Formate dehydrogenase, C-terminal domain superfamily / Formate dehydrogenase N, transmembrane / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit ...Single helix bin / Formate dehydrogenase iron-sulphur subunit, Proteobacteria / Formate dehydrogenase, gamma subunit / Formate dehydrogenase iron-sulphur subunit / Formate dehydrogenase, transmembrane / Formate dehydrogenase, C-terminal domain superfamily / Formate dehydrogenase N, transmembrane / Cytochrome b561, bacterial/Ni-hydrogenase / Prokaryotic cytochrome b561 / Fumarate Reductase Cytochrome B subunit / Transmembrane di-heme cytochromes, Chain C / Formate dehydrogenase-N, alpha subunit / 4Fe-4S binding domain / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 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 oxidoreductase Fe4S4 domain / 4Fe-4S binding domain / Alpha-Beta Plaits - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Di-haem cytochrome, transmembrane / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Plaits / Up-down Bundle / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / CARDIOLIPIN / PROTOPORPHYRIN IX CONTAINING FE / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / Chem-MGD / IRON/SULFUR CLUSTER / Formate dehydrogenase, nitrate-inducible, iron-sulfur subunit / Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit / Formate dehydrogenase, nitrate-inducible, major subunit / Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJormakka, M. / Tornroth, S. / Byrne, B. / Iwata, S.
CitationJournal: Science / Year: 2002
Title: Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.
Authors: Jormakka, M. / Tornroth, S. / Byrne, B. / Iwata, S.
History
DepositionJan 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 19, 2014Group: Atomic model / Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.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_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: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
B: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
C: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,06515
Polymers170,7733
Non-polymers6,29212
Water35,7421984
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A: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
B: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
C: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
hetero molecules

A: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
B: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
C: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
hetero molecules

A: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT
B: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
C: FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,19545
Polymers512,3209
Non-polymers18,87536
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area73750 Å2
ΔGint-824 kcal/mol
Surface area134850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)203.000, 203.000, 203.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-1041-

HOH

21C-593-

HOH

31C-1732-

HOH

DetailsBiological assembly is a trimer, related by a crystallographic 3-fold axis.

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Components

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FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, ... , 3 types, 3 molecules ABC

#1: Protein FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, MAJOR SUBUNIT / / E.C.1.2.1.2 / FORMATE DEHYDROGENASE-N ALPHA SUBUNIT / FDH-N ALPHA SUBUNIT / ANAEROBIC FORMATE DEHYDROGENASE MAJOR SUBUNIT


Mass: 113088.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: GL101 / References: UniProt: P24183, formate dehydrogenase
#2: Protein FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT / / E.C.1.2.1.2 / FORMATE DEHYDROGENASE-N BETA SUBUNIT / FDH-N BETA SUBUNIT / ANAEROBIC FORMATE DEHYDROGENASE IRON- ...FORMATE DEHYDROGENASE-N BETA SUBUNIT / FDH-N BETA SUBUNIT / ANAEROBIC FORMATE DEHYDROGENASE IRON-SULFUR SUBUNIT


Mass: 32279.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: GL101 / References: UniProt: P0AAJ3, formate dehydrogenase
#3: Protein FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, CYTOCHROME B556(FDN) SUBUNIT / / E.C.1.2.1.2 / FORMATE DEHYDROGENASE-N GAMMA SUBUNIT / FDH-N GAMMA SUBUNIT / ANAEROBIC FORMATE DEHYDROGENASE ...FORMATE DEHYDROGENASE-N GAMMA SUBUNIT / FDH-N GAMMA SUBUNIT / ANAEROBIC FORMATE DEHYDROGENASE CYTOCHROME B556 SUBUNIT


Mass: 25405.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HQNO Complex / Source: (natural) Escherichia coli (E. coli) / Strain: GL101
References: UniProt: P24185, UniProt: P0AEK7*PLUS, formate dehydrogenase

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Non-polymers , 7 types, 1996 molecules

#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#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.: 2 / 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-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#8: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical ChemComp-HQO / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / 2-HEPTYL-1-OXY-QUINOLIN-4-OL


Mass: 259.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1984 / 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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115-20 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 %OG1drop
4100 mMHEPES1reservoirpH7.5-8.2
56-12 %(w/v)PEG15001reservoir
6100 mM1reservoirNaCl
7100 mM1reservoirMgCl2
85 %ethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 25, 2000 / Details: Micro Diffractometer
RadiationMonochromator: [111] reflection from thin diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 61817 / % possible obs: 0.908 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -0.3 / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.088
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.209 / % possible all: 74.9

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4055803.56 / 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
Rfree0.239 542 1 %RANDOM
Rwork0.198 ---
all0.198 61817 --
obs0.198 61817 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.9312 Å2 / ksol: 0.315942 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11709 0 310 1984 14003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d3.6
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 66 1.1 %
Rwork0.332 5707 -
obs--74.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FS4+MGD+HEM.PARWATER.TOP
X-RAY DIFFRACTION3CLL+HQNO.PARAMFS4+MGD+HEM.TOP
X-RAY DIFFRACTION4ION.PARAMCDL.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMION.TOP
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.6

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