[English] 日本語
Yorodumi
- PDB-3wr5: Structural basis on the efficient CO2 reduction of acidophilic fo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wr5
TitleStructural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase
Similarity search - Component
Biological speciesThiobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.142 Å
AuthorsHa, J.M. / Jeon, S.T. / Yoon, H.J. / Lee, H.H.
CitationJournal: To be Published
Title: Structural basis on the efficient CO2 reduction of acidophilic formate dehydrogenase
Authors: Ha, J.M. / Jeon, S.T. / Yoon, H.J. / Lee, H.H.
History
DepositionFeb 16, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formate dehydrogenase
B: Formate dehydrogenase
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,9247
Polymers177,9344
Non-polymers1,9903
Water17,511972
1
A: Formate dehydrogenase
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2944
Polymers88,9672
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-56 kcal/mol
Surface area26670 Å2
MethodPISA
2
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6303
Polymers88,9672
Non-polymers6631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8840 Å2
ΔGint-46 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.942, 72.729, 386.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA-3 - 399
211chain BB-2 - 399
311chain CC-4 - 399
411chain DD-1 - 374

-
Components

#1: Protein
Formate dehydrogenase


Mass: 44483.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiobacillus (bacteria) / Strain: KNK65MA / Gene: fdh65MA / Production host: Escherichia coli (E. coli) / References: UniProt: Q76EB7, formate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4M Lithium chloride, 0.1M Tris-HCl pH 7.5, 24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jan 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 88253 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.48 Å2
Reflection shellResolution: 2.14→2.18 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NAD

2nad


Resolution: 2.142→42.25 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 4407 5.01 %
Rwork0.1723 --
obs0.1742 87926 99.58 %
all-88253 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.8246 Å2
Refinement stepCycle: LAST / Resolution: 2.142→42.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12146 0 132 972 13250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912593
X-RAY DIFFRACTIONf_angle_d1.35517152
X-RAY DIFFRACTIONf_dihedral_angle_d14.1454752
X-RAY DIFFRACTIONf_chiral_restr0.0631883
X-RAY DIFFRACTIONf_plane_restr0.0082209
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7334X-RAY DIFFRACTION6.112TORSIONAL
12B7334X-RAY DIFFRACTION6.112TORSIONAL
13C7334X-RAY DIFFRACTION6.112TORSIONAL
14D7334X-RAY DIFFRACTION6.112TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1424-2.16670.24021480.20992523267194
2.1667-2.19220.27531590.215327432902100
2.1922-2.21890.25781470.213827502897100
2.2189-2.2470.25321420.210227672909100
2.247-2.27660.2561570.213427342891100
2.2766-2.30780.26011510.210427252876100
2.3078-2.34070.25541320.201928252957100
2.3407-2.37570.24511550.192826852840100
2.3757-2.41280.22711490.182928132962100
2.4128-2.45230.23971380.190527322870100
2.4523-2.49460.20161450.18827532898100
2.4946-2.540.24781650.192827942959100
2.54-2.58880.22661450.19227382883100
2.5888-2.64170.2911210.191227952916100
2.6417-2.69910.23211490.190127892938100
2.6991-2.76190.25461210.189827692890100
2.7619-2.83090.25181520.181227782930100
2.8309-2.90750.21181440.187527982942100
2.9075-2.9930.2311510.18727642915100
2.993-3.08960.25591440.184927932937100
3.0896-3.19990.1971590.172427702929100
3.1999-3.3280.21161520.177928272979100
3.328-3.47940.2141560.16427832939100
3.4794-3.66280.17331620.153227952957100
3.6628-3.89210.18251500.14827992949100
3.8921-4.19240.16271350.140828402975100
4.1924-4.61380.15981360.1332864300099
4.6138-5.28030.15781560.14522827298399
5.2803-6.64850.20581260.17862930305699
6.6485-42.25840.17191600.15463016317698

+
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