[English] 日本語
Yorodumi
- PDB-2eez: Crystal structure of alanine dehydrogenase from themus thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2eez
TitleCrystal structure of alanine dehydrogenase from themus thermophilus
ComponentsAlanine dehydrogenase
KeywordsOXIDOREDUCTASE / alanine dehydrogenase / thermus / ttha0216 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding / plasma membrane
Similarity search - Function
Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain ...Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-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
Alanine dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsKumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of alanine dehydrogenase from themus thermophilus
Authors: Kumarevel, T.S. / Karthe, P. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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: Alanine dehydrogenase
C: Alanine dehydrogenase
D: Alanine dehydrogenase
E: Alanine dehydrogenase
F: Alanine dehydrogenase
G: Alanine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)232,0546
Polymers232,0546
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-45 kcal/mol
Surface area72890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.940, 133.240, 147.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Alanine dehydrogenase


Mass: 38675.641 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ttha0216 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q5SLS7, alanine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1M 1,6 hexanediol, 0.1M Na acetate, 5mM Cobalt chloride, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 8, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 71336 / Num. obs: 71336 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.361 / Num. unique all: 7029 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SAY

1say


Resolution: 2.71→19.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2923035.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3600 5.1 %RANDOM
Rwork0.22 ---
obs0.22 71073 98.9 %-
all-71336 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9191 Å2 / ksol: 0.333665 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.95 Å20 Å20 Å2
2---1.73 Å20 Å2
3---5.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.71→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15138 0 0 384 15522
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 525 5.1 %
Rwork0.262 9851 -
obs--86.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

+
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