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- PDB-1pby: Structure of the Phenylhydrazine Adduct of the Quinohemoprotein A... -

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Basic information

Entry
Database: PDB / ID: 1pby
TitleStructure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution
Components(quinohemoprotein amine dehydrogenase ...) x 3
KeywordsOXIDOREDUCTASE / QUINOHEMOPROTEIN / AMINE DEHYDROGENASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With a cytochrome as acceptor / oxidoreductase activity, acting on the CH-NH2 group of donors / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit ...Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain superfamily / Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 superfamily / : / Quinohemoprotein amine dehydrogenase, gamma subunit / Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, alpha subunit domain II / : / Quinoprotein amine dehydrogenase, beta chain-like / Cytochrome c-like domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Lipocalin / Few Secondary Structures / Irregular / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
HEME C / TERTIARY-BUTYL ALCOHOL / : / : / Quinohemoprotein amine dehydrogenase 40 kDa subunit / Quinohemoprotein amine dehydrogenase subunit gamma / Quinohemoprotein amine dehydrogenase 60 kDa subunit
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / refined directly / Resolution: 1.7 Å
AuthorsDatta, S. / Ikeda, T. / Kano, K. / Mathews, F.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution.
Authors: Datta, S. / Ikeda, T. / Kano, K. / Mathews, F.S.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of a quinohemoprotein amine dehydrogenase with an uncommon redox cofactor and highly unusual crosslinking
History
DepositionMay 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: quinohemoprotein amine dehydrogenase 60 kDa subunit
B: quinohemoprotein amine dehydrogenase 40 kDa subunit
C: quinohemoprotein amine dehydrogenase 9 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1119
Polymers98,5773
Non-polymers1,5336
Water23,3291295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-83 kcal/mol
Surface area33450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.237, 99.237, 213.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Quinohemoprotein amine dehydrogenase ... , 3 types, 3 molecules ABC

#1: Protein quinohemoprotein amine dehydrogenase 60 kDa subunit


Mass: 52711.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / Strain (production host): IFO12442 / References: UniProt: Q8VUT0, EC: 1.4.99.3
#2: Protein quinohemoprotein amine dehydrogenase 40 kDa subunit


Mass: 37021.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / References: GenBank: 17402571, UniProt: Q8VUS7*PLUS
#3: Protein quinohemoprotein amine dehydrogenase 9 kDa subunit


Mass: 8843.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Production host: Paracoccus denitrificans (bacteria) / References: GenBank: 17402570, UniProt: Q8VUS8*PLUS

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Non-polymers , 3 types, 1301 molecules

#4: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#5: Chemical
ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1295 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, sodium citrate, t-butyl alcohol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium citrate1reservoirpH5.6
218 %PEG40001reservoir
321 %t-butyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→36.24 Å / Num. all: 117161 / Num. obs: 110131 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8700 / % possible all: 75.4
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 75.4 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: refined directly
Starting model: PDB ENTRY 1JJU

1jju


Resolution: 1.7→36.42 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 10633 10 %RANDOM
Rwork0.191 ---
all-117339 --
obs-105982 90.2 %-
Displacement parametersBiso mean: 22.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 86 1315 8443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.7-1.810.282312929.80.2652119450.0081185468.6
1.81-1.950.258716480.227614828
1.95-2.140.236617940.201116479
2.14-2.450.233719010.194516848
2.45-3.090.230519730.192417373
3.09-36.420.198720250.171217967
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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