[English] 日本語
Yorodumi
- PDB-6vdh: Crystal structure of ancestral apicomplexan lactate dehydrogenase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vdh
TitleCrystal structure of ancestral apicomplexan lactate dehydrogenase in alternate dimer configuration with sulfate.
Componentslactate dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding / Rossman Fold / Ancestral Reconstruction
Function / homologyL-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesApicomplexa sp. (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTheobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM096053 United States
CitationJournal: To Be Published
Title: Mechanism of Bifunctionality in an Ancestral Apicomplexan Malate/Lactate Dehydrogenase
Authors: Theobald, D.L. / Wirth, J.D. / Classen, S. / Perlmutter, N.
History
DepositionDec 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0034
Polymers71,8112
Non-polymers1922
Water5,819323
1
A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules

A: lactate dehydrogenase
B: lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0068
Polymers143,6224
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area17220 Å2
ΔGint-135 kcal/mol
Surface area42850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.380, 105.440, 151.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein lactate dehydrogenase /


Mass: 35905.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ancestral apicomplexan lactate dehydrogenase in alternate dimer conformation with sulfate bound
Source: (gene. exp.) Apicomplexa sp. (eukaryote) / Plasmid: pET24a(+) / Production host: Escherichia coli BL21 (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20mg/mL protein, 2mM NADH4; well solution: 5% v/v 2-Propanol, 2.5M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115866 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115866 Å / Relative weight: 1
ReflectionResolution: 1.68→45.53 Å / Num. obs: 86980 / % possible obs: 88.9 % / Redundancy: 5.92 % / Biso Wilson estimate: 30.34 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.102 / Χ2: 0.86 / Net I/σ(I): 3.66
Reflection shellResolution: 1.68→1.79 Å / Redundancy: 3.18 % / Mean I/σ(I) obs: 0.18 / Num. unique obs: 18335 / CC1/2: 0.071 / Rrim(I) all: 5.295 / % possible all: 62.6

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLG

4plg


Resolution: 1.85→45.53 Å / SU ML: 0.3457 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.0699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2362 1533 2.34 %
Rwork0.2095 63961 -
obs0.2101 65494 92.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.49 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 10 323 5059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374812
X-RAY DIFFRACTIONf_angle_d0.5926512
X-RAY DIFFRACTIONf_chiral_restr0.046763
X-RAY DIFFRACTIONf_plane_restr0.0036835
X-RAY DIFFRACTIONf_dihedral_angle_d4.6525661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.57191080.52024194X-RAY DIFFRACTION67.96
1.91-1.980.61721200.57495093X-RAY DIFFRACTION82.28
1.98-2.060.26371490.23666240X-RAY DIFFRACTION99.92
2.06-2.150.25981440.21736249X-RAY DIFFRACTION99.95
2.15-2.260.37071190.32974914X-RAY DIFFRACTION79.33
2.26-2.410.27681380.2295659X-RAY DIFFRACTION89.99
2.41-2.590.24781460.19336237X-RAY DIFFRACTION99.98
2.59-2.850.22341450.19076289X-RAY DIFFRACTION100
2.85-3.270.18871580.19056262X-RAY DIFFRACTION100
3.27-4.110.20451420.18476298X-RAY DIFFRACTION98.94
4.11-45.530.20121640.17436526X-RAY DIFFRACTION99.78

+
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