[English] 日本語
Yorodumi
- PDB-5hs4: Plasmdoium Vivax Lactate dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hs4
TitlePlasmdoium Vivax Lactate dehydrogenase
ComponentsL-lactate dehydrogenaseLactate dehydrogenase
KeywordsOXIDOREDUCTASE / malaria / lactate dehydrogenase / LDH
Function / homology
Function and homology information


carboxylic acid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
Malate dehydrogenase, type 3 / 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 / NAD(P)-binding Rossmann-like Domain ...Malate dehydrogenase, type 3 / 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 / 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 speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.339 Å
AuthorsChoi, S.J. / Ban, C.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF- 2015027587 Korea, Republic Of
National Research Foundation of KoreaNRF-2014K1B1A1073720 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition
Authors: Choi, S.J. / Ban, C.
History
DepositionJan 25, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)37,6601
Polymers37,6601
Non-polymers00
Water3,963220
1
A: L-lactate dehydrogenase

A: L-lactate dehydrogenase

A: L-lactate dehydrogenase

A: L-lactate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)150,6394
Polymers150,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area15510 Å2
ΔGint-90 kcal/mol
Surface area39460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.792, 80.613, 93.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-477-

HOH

21A-618-

HOH

-
Components

#1: Protein L-lactate dehydrogenase / Lactate dehydrogenase / Lactate dehydrogenase / Parasite lactate dehydrogenase


Mass: 37659.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: LDH / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q4PRK9, L-lactate dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.89 Å3/Da / Density % sol: 35.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: ammonium nitrate, PEG-3350, magnesium ion, potassium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.3388→25 Å / Num. obs: 63845 / % possible obs: 99.2 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.65 Å2 / Rmerge(I) obs: 0.076 / Net I/av σ(I): 78.446 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.34-1.368.80.274197.3
1.36-1.399.20.254198.1
1.39-1.419.50.242198.4
1.41-1.449.60.227198.6
1.44-1.4710.10.21199
1.47-1.5110.50.198199
1.51-1.5510.80.186199.1
1.55-1.5911.10.174199.5
1.59-1.6411.40.16199.5
1.64-1.6911.50.153199.5
1.69-1.7511.90.14199.7
1.75-1.8212.40.128199.7
1.82-1.912.60.12199.6
1.9-213.10.107199.9
2-2.1313.50.0991100
2.13-2.2913.80.0961100
2.29-2.5213.90.0951100
2.52-2.8913.90.0781100
2.89-3.6313.90.062199.9
3.63-2513.50.051197.1

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A92
Resolution: 1.339→23.765 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.54 / Phase error: 14.37
RfactorNum. reflection% reflection
Rfree0.1714 3230 5.06 %
Rwork0.1499 --
obs0.151 63843 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.09 Å2 / Biso mean: 17.8068 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 1.339→23.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 0 220 2500
Biso mean---26.14 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082316
X-RAY DIFFRACTIONf_angle_d1.1633135
X-RAY DIFFRACTIONf_chiral_restr0.041382
X-RAY DIFFRACTIONf_plane_restr0.005398
X-RAY DIFFRACTIONf_dihedral_angle_d11.813865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3388-1.35880.17791180.13942413253193
1.3588-1.380.18431360.13862598273498
1.38-1.40270.16611340.13342590272498
1.4027-1.42680.17471280.13682596272499
1.4268-1.45280.15891200.13072650277099
1.4528-1.48070.18011420.12352591273399
1.4807-1.51090.1471540.12332608276299
1.5109-1.54380.17521300.12772633276399
1.5438-1.57970.17561500.12022620277099
1.5797-1.61920.15641490.12172604275399
1.6192-1.6630.15941450.12282607275299
1.663-1.71190.16161230.126526822805100
1.7119-1.76710.1631400.134226502790100
1.7671-1.83030.16421440.135326252769100
1.8303-1.90350.16181230.1526912814100
1.9035-1.99010.18171700.151926132783100
1.9901-2.0950.1571330.149626602793100
2.095-2.22610.1931330.146426912824100
2.2261-2.39790.14811460.155226602806100
2.3979-2.63890.17271610.165526742835100
2.6389-3.02010.19771520.173627112863100
3.0201-3.80250.18721560.160727052861100
3.8025-23.76880.15681430.15422741288497

+
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