[English] 日本語
Yorodumi
- PDB-6j9d: Babesia microti lactate dehydrogenase R99A (BmLDHR99A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j9d
TitleBabesia microti lactate dehydrogenase R99A (BmLDHR99A)
ComponentsL-lactate dehydrogenaseLactate dehydrogenase
KeywordsOXIDOREDUCTASE / BmLDH
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain ...L-lactate dehydrogenase active site. / L-lactate dehydrogenase / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Prokaryotic membrane lipoprotein lipid attachment site profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-lactate dehydrogenase
Similarity search - Component
Biological speciesBabesia microti
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsYu, L.
CitationJournal: Faseb J. / Year: 2019
Title: Crystal structures ofBabesia microtilactate dehydrogenase BmLDH reveal a critical role for Arg99 in catalysis.
Authors: Yu, L. / Shen, Z. / Liu, Q. / Zhan, X. / Luo, X. / An, X. / Sun, Y. / Li, M. / Wang, S. / Nie, Z. / Ao, Y. / Zhao, Y. / Peng, G. / Mamoun, C.B. / He, L. / Zhao, J.
History
DepositionJan 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)67,7152
Polymers67,7152
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.332, 147.332, 65.773
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein L-lactate dehydrogenase / Lactate dehydrogenase


Mass: 33857.254 Da / Num. of mol.: 2 / Mutation: R99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia microti (strain RI) (eukaryote)
Strain: RI / Gene: BMR1_01G00020 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: I7J7V6, L-lactate dehydrogenase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium Chloride, 0.1 M Tris:HCl pH 8.5, 15-18% (w/v) PEG 4000.

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 160 kV / Wavelength: 0.9789 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. obs: 18199 / % possible obs: 98.9 % / Redundancy: 13 % / CC1/2: 0.989 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.038 / Rrim(I) all: 0.081 / Net I/σ(I): 2.69
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 2.69 / Num. unique obs: 18429 / CC1/2: 0.989 / Rpim(I) all: 0.038 / Rrim(I) all: 0.081 / Χ2: 1.271

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000V718data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.904→35.715 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.38
RfactorNum. reflection% reflection
Rfree0.3217 859 4.73 %
Rwork0.2894 --
obs0.2909 18178 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.48 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 2.904→35.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 0 0 3970
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054022
X-RAY DIFFRACTIONf_angle_d0.6925425
X-RAY DIFFRACTIONf_chiral_restr0.048658
X-RAY DIFFRACTIONf_plane_restr0.003671
X-RAY DIFFRACTIONf_dihedral_angle_d17.8731474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.904-3.08590.35291620.2893279698
3.0859-3.3240.33011280.28932904100
3.324-3.65820.36981480.2893289899
3.6582-4.18690.33391380.2768287499
4.1869-5.27230.28931310.2625288998
5.27230.30951520.2893295898
Refinement TLS params.Method: refined / Origin x: -37.7717 Å / Origin y: 38.0962 Å / Origin z: -7.5983 Å
111213212223313233
T0.4869 Å2-0.0679 Å20.0299 Å2-0.3751 Å20.0198 Å2--0.3062 Å2
L3.2029 °20.2796 °20.6489 °2-2.4729 °20.0307 °2--1.7593 °2
S0.1985 Å °-0.0281 Å °-0.2814 Å °0.4188 Å °-0.2096 Å °0.0076 Å °0.4405 Å °-0.0441 Å °0.0349 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 327
2X-RAY DIFFRACTION1allB23 - 321

+
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