[English] 日本語
Yorodumi
- PDB-3naq: Apo-form of NAD-dependent formate dehydrogenase from higher-plant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3naq
TitleApo-form of NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / NAD-dependent formate dehydroganase / homodimer / apo-form
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / thylakoid / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / plastid / chloroplast / NAD binding / mitochondrion / cytosol
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
Formate dehydrogenase, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsShabalin, I.G. / Polyakov, K.M. / Serov, A.E. / Skirgello, O.E. / Sadykhov, E.G. / Dorovatovskiy, P.V. / Tishkov, V.I. / Popov, V.O.
CitationJournal: to be published
Title: Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana
Authors: Shabalin, I.G. / Polyakov, K.M. / Skirgello, O.E. / Tishkov, V.I. / Popov, V.O.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6858
Polymers79,1082
Non-polymers5766
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-103 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.330, 106.230, 106.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Formate dehydrogenase / NAD-dependent formate dehydrogenase / FDH


Mass: 39554.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g14780, FDH, FDH1, T9L3_80 / Plasmid: p1AraFDH / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9S7E4, formate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution (2ul): 6 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA. Reservoir solution (2ul): 0.1M Bis-Tris, pH 6.0, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.7→75.16 Å / Num. obs: 87821 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.046 / Net I/σ(I): 31.25
Reflection shellResolution: 1.7→1.8 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 5.36 / % possible all: 90.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→75.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.563 / SU ML: 0.068 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19718 4407 5 %RANDOM
Rwork0.16747 ---
obs0.16894 83414 99.43 %-
all-83414 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.692 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å20 Å20 Å2
2--1.9 Å20 Å2
3---1.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.231 Å
Refinement stepCycle: LAST / Resolution: 1.7→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 30 559 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225580
X-RAY DIFFRACTIONr_bond_other_d0.0010.023730
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9737568
X-RAY DIFFRACTIONr_angle_other_deg0.97739132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78424.426244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92515954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1821532
X-RAY DIFFRACTIONr_chiral_restr0.10.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021070
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8861.53484
X-RAY DIFFRACTIONr_mcbond_other0.3041.51428
X-RAY DIFFRACTIONr_mcangle_it1.4725603
X-RAY DIFFRACTIONr_scbond_it2.41832096
X-RAY DIFFRACTIONr_scangle_it3.7314.51965
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 322 -
Rwork0.238 6006 -
obs--98.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2544-0.3913-0.31161.55250.86651.11550.03120.07510.1612-0.17010.0278-0.0255-0.10640.0175-0.0590.1836-0.00150.00840.0331-0.00460.092338.909-1.0586.016
24.9173-0.3562-0.4351.08930.05050.8801-0.19560.9378-0.471-0.09290.03190.02970.131-0.15060.16370.1504-0.04730.04010.217-0.13580.12075.63-2.15111.743
31.3096-0.0475-0.19881.22340.29130.9854-0.0534-0.17-0.06950.02940.0367-0.00350.1575-0.0210.01670.2083-0.00610.00660.0681-0.00390.135634.479-10.68214.37
41.2227-0.3087-0.33621.28710.94281.62170.0290.15520.0719-0.1235-0.05290.0053-0.1851-0.01170.02390.1810.0071-0.00060.04650.00080.0755-21.31520.56527.726
54.8378-0.5239-0.33110.82670.08531.1733-0.1939-0.48310.94080.11850.1535-0.1429-0.09590.03010.04030.15120.0395-0.04770.0806-0.13690.268711.87614.80428.732
61.6831-0.2229-0.2381.05690.34291.2739-0.0268-0.0629-0.19340.17360.009-0.04240.03090.00090.01780.19690.0071-0.00940.0750.00150.104-16.89212.19137.347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 145
2X-RAY DIFFRACTION2A146 - 332
3X-RAY DIFFRACTION3A333 - 378
4X-RAY DIFFRACTION4B28 - 145
5X-RAY DIFFRACTION5B146 - 332
6X-RAY DIFFRACTION6B333 - 378

+
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://pdbjlvh1.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