[English] 日本語
Yorodumi
- PDB-6de6: 2.1 A resolution structure of histamine dehydrogenase from Rhizob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6de6
Title2.1 A resolution structure of histamine dehydrogenase from Rhizobium sp. 4-9
ComponentsHistamine dehydrogenase
KeywordsOXIDOREDUCTASE / histamine dehydrogenase / FMN binding / 4Fe-4S cluster
Function / homology
Function and homology information


FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / : / OYE-like second alpha/beta domain / : / NAD(P)-binding Rossmann-like domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / IRON/SULFUR CLUSTER / Histamine dehydrogenase
Similarity search - Component
Biological speciesRhizobium sp. 4-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGoyal, P. / Lovell, S. / Richter, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor.
Authors: Goyal, P. / Deay 3rd, D. / Seibold, S. / Candido, A.C.L. / Lovell, S. / Battaile, K.P. / Wilson, G.S. / Richter, M.L. / Petillo, P.A.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr1_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histamine dehydrogenase
B: Histamine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7669
Polymers154,2012
Non-polymers2,5657
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-98 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.223, 105.314, 140.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 130 or (resid 131...
21(chain B and ((resid 4 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHR(chain A and (resid 4 through 130 or (resid 131...AA4 - 1307 - 133
12PHEPHEPHEPHE(chain A and (resid 4 through 130 or (resid 131...AA131134
13ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
14ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
15ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
16ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
21ASNASNASNASN(chain B and ((resid 4 and (name N or name...BB47
22ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
23ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
24ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
25ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
26ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Histamine dehydrogenase


Mass: 77100.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. 4-9 (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60I59

-
Non-polymers , 5 types, 561 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.16 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na HEPES, 18% w/v PEG 12000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.43 Å / Num. obs: 89613 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 12.7 / Num. measured all: 586744 / Scaling rejects: 82
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.222 / Num. unique obs: 4554 / CC1/2: 0.64 / Rpim(I) all: 0.519 / Rrim(I) all: 1.329 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.09 Å48.43 Å
Translation5.09 Å48.43 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k30

3k30


Resolution: 2.1→48.427 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.2022 4463 4.99 %
Rwork0.164 --
obs0.166 89514 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.52 Å2 / Biso mean: 37.0718 Å2 / Biso min: 20.17 Å2
Refinement stepCycle: final / Resolution: 2.1→48.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 137 554 10994
Biso mean--35.05 37.87 -
Num. residues----1341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6002X-RAY DIFFRACTION6.227TORSIONAL
12B6002X-RAY DIFFRACTION6.227TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.27691530.232227682921100
2.1239-2.14890.28261500.230128382988100
2.1489-2.17510.2771280.221327872915100
2.1751-2.20260.25471590.211228262985100
2.2026-2.23160.2721720.213827702942100
2.2316-2.26210.28361460.240727862932100
2.2621-2.29450.26261230.194928692992100
2.2945-2.32870.24031480.192527622910100
2.3287-2.36510.23431470.179828112958100
2.3651-2.40390.23991300.177728392969100
2.4039-2.44530.23151610.174427922953100
2.4453-2.48980.24631350.173428152950100
2.4898-2.53770.22131540.164428092963100
2.5377-2.58950.22041530.163728252978100
2.5895-2.64580.18981620.162628062968100
2.6458-2.70730.21981090.161528602969100
2.7073-2.7750.19131310.167128552986100
2.775-2.850.21881430.168728242967100
2.85-2.93390.23251550.170628262981100
2.9339-3.02860.21261580.170228142972100
3.0286-3.13680.20631630.176928302993100
3.1368-3.26240.22961450.188728332978100
3.2624-3.41080.21121740.170728192993100
3.4108-3.59060.2051380.168428512989100
3.5906-3.81540.18421740.148128303004100
3.8154-4.10990.18021670.137728403007100
4.1099-4.52320.14281300.124529113041100
4.5232-5.17710.1381610.119828803041100
5.1771-6.52010.16721470.156229333080100
6.5201-48.44010.21811470.17453042318999

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more