[English] 日本語
Yorodumi
- PDB-3wx0: The crystal structure of D-lactate dehydrogenase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wx0
TitleThe crystal structure of D-lactate dehydrogenase from Escherichia coli
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
KeywordsOXIDOREDUCTASE / Rossmann Fold / Dehydrogenase / NADH binding
Function / homology
Function and homology information


D-lactate dehydrogenase / D-lactate dehydrogenase activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol
Similarity search - Function
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 ...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
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding / D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsFurukawa, N. / Togawa, M. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
CitationJournal: To be Published
Title: Allosteric D-lactate dehydrogenases from three Gram-negative bacteria
Authors: Furukawa, N. / Togawa, M. / Miyanaga, A. / Nakajima, M. / Taguchi, H.
History
DepositionJul 8, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
B: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
C: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding
D: D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding


Theoretical massNumber of molelcules
Total (without water)154,3844
Polymers154,3844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.029, 131.029, 405.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLYAA4 - 32120 - 337
21ALAALACYSCYSBB4 - 32420 - 340
12ALAALAASNASNAA4 - 31420 - 330
22ALAALAASNASNCC4 - 31420 - 330
13LEULEUASNASNAA3 - 31719 - 333
23LEULEUASNASNDD3 - 31719 - 333
14ALAALAASNASNBB4 - 31420 - 330
24ALAALAASNASNCC4 - 31420 - 330
15ALAALASERSERBB4 - 31620 - 332
25ALAALASERSERDD4 - 31620 - 332
16ALAALAASNASNCC4 - 31420 - 330
26ALAALAASNASNDD4 - 31420 - 330

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding / D-lactate dehydrogenase / D-2-hydroxyacid dehydrogenase


Mass: 38595.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: B21_01364, ECBD_2243, ECD_01352, ldhA / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3)
References: UniProt: C6EEW4, UniProt: A0A140N893*PLUS, D-lactate dehydrogenase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate (pH 4.5), 0.8M sodium dihydrogenphosphate, 1.2M potassium monohydrogen phosphate., VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→55.03 Å / Num. all: 32130 / Num. obs: 32128 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.48 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J49

1j49


Resolution: 3.3→55.03 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.867 / SU B: 20.876 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27116 1631 5.1 %RANDOM
Rwork0.23143 ---
obs0.23347 30412 99.95 %-
all-32046 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.62 Å20 Å2
2--0.62 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→55.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 0 0 8746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198926
X-RAY DIFFRACTIONr_bond_other_d0.0050.028615
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.96312041
X-RAY DIFFRACTIONr_angle_other_deg1.071319750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93924.272405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.078151543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6691550
X-RAY DIFFRACTIONr_chiral_restr0.080.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210115
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022073
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_it5.1467.2324511
X-RAY DIFFRACTIONr_mcbond_other5.1437.2324510
X-RAY DIFFRACTIONr_mcangle_it8.00210.8385609
X-RAY DIFFRACTIONr_mcangle_other8.00210.8385610
X-RAY DIFFRACTIONr_scbond_it5.1447.654414
X-RAY DIFFRACTIONr_scbond_other5.1437.654415
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.27911.3436432
X-RAY DIFFRACTIONr_long_range_B_refined11.06357.3029914
X-RAY DIFFRACTIONr_long_range_B_other11.06357.3049915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161720.07
12B161720.07
21A161930.07
22C161930.07
31A177840.06
32D177840.06
41B144800.09
42C144800.09
51B154350.08
52D154350.08
61C155530.07
62D155530.07
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 129 -
Rwork0.306 2166 -
obs--100 %

+
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