[English] 日本語
Yorodumi
- PDB-2xxb: Penta-mutant of Thermus thermophilus lactate dehydrogenase, compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xxb
TitlePenta-mutant of Thermus thermophilus lactate dehydrogenase, complex with AMP
ComponentsL-LACTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HYPERTHERMOPHILE
Function / homology
Function and homology information


L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / glycolytic 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 / 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
ADENOSINE MONOPHOSPHATE / L-lactate dehydrogenase
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDiop, F. / Coquelle, N. / Vellieux, F.M.D.
CitationJournal: To be Published
Title: Lactate Dehydrogenase from T. Thermophilus, Penta-Mutant (Complex with AMP)
Authors: Diop, F. / Coquelle, N. / Vellieux, F.M.D.
History
DepositionNov 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8934
Polymers65,1992
Non-polymers6942
Water5,278293
1
A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules

A: L-LACTATE DEHYDROGENASE
B: L-LACTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7868
Polymers130,3974
Non-polymers1,3894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area13000 Å2
ΔGint-81.8 kcal/mol
Surface area45420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.990, 153.470, 150.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein L-LACTATE DEHYDROGENASE / L-LDH


Mass: 32599.373 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 79 TO TRP ENGINEERED RESIDUE IN CHAIN A, ARG 151 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 79 TO TRP ENGINEERED RESIDUE IN CHAIN A, ARG 151 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 299 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 313 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 79 TO TRP ENGINEERED RESIDUE IN CHAIN B, ARG 151 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 279 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 299 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 313 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROPS, 2 MICROL PROTEIN AND 2 MICROL PRECIPITANT. 0.1 M BICINE, 1 M LICL, 15% PEG 6000 PH 9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.15→48.97 Å / Num. obs: 32767 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Redundancy: 7.29 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.64
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 7.02 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.3 / % possible all: 72.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6M

2v6m


Resolution: 2.15→48.956 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 28.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 1638 5 %
Rwork0.2191 --
obs0.2227 32759 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.936 Å2 / ksol: 0.307 e/Å3
Displacement parametersBiso mean: 31.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.8104 Å2-0 Å20 Å2
2---4.1626 Å2-0 Å2
3---0.3522 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 46 293 4939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084768
X-RAY DIFFRACTIONf_angle_d1.1426512
X-RAY DIFFRACTIONf_dihedral_angle_d17.3261700
X-RAY DIFFRACTIONf_chiral_restr0.071765
X-RAY DIFFRACTIONf_plane_restr0.004842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1502-2.22710.391210.33252314X-RAY DIFFRACTION71
2.2271-2.31630.69891330.48412515X-RAY DIFFRACTION76
2.3163-2.42170.31651700.21563237X-RAY DIFFRACTION98
2.4217-2.54930.29161710.19813257X-RAY DIFFRACTION98
2.5493-2.70910.30671720.21153257X-RAY DIFFRACTION99
2.7091-2.91820.28311730.20913285X-RAY DIFFRACTION99
2.9182-3.21180.2661730.20473290X-RAY DIFFRACTION99
3.2118-3.67650.29271690.2023214X-RAY DIFFRACTION96
3.6765-4.63140.22551720.15863270X-RAY DIFFRACTION96
4.6314-48.96870.16811840.13693482X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.12440.1462-0.03991.2107-0.80410.9911-0.0624-0.1426-0.08180.1922-0.0504-0.1491-0.12270.09130.1090.0273-0.0190.00350.14120.03630.06954.5198-31.7515-14.3852
20.1361-0.0690.09780.5984-0.49570.96040.0510.0121-0.01270.3287-0.1767-0.1207-0.39340.15630.25610.1369-0.0889-0.10660.05910.03120.08112.9253-14.201-18.1969
30.1991-0.06090.27410.9647-0.48351.2017-0.069-0.03530.02520.2582-0.1411-0.1095-0.34950.0340.14220.1153-0.0438-0.03410.0499-0.00090.0538-3.0931-10.6441-24.5813
40.4175-0.38-0.17613.2355-1.03030.57420.1564-0.08650.16521.2987-0.1613-0.0458-0.42760.12420.06290.6011-0.2062-0.02940.0792-0.00710.13063.9157-1.4533-15.189
50.33330.1411-0.41210.32280.1010.8567-0.0390.06650.12080.03290.01280.09430.0249-0.23530.02260.0145-0.03030.01090.16580.00240.0891-17.976-33.1459-21.0206
60.45080.2916-0.06320.65460.01180.55850.0298-0.04630.092-0.0451-0.0287-0.0180.149-0.1871-0.00550.039-0.03460.01290.08140.00310.044-11.9088-50.7436-25.4835
70.4285-0.09630.02470.0301-0.10111.04880.02560.0104-0.0421-0.038-0.07290.00250.1960.08020.03460.0449-0.0277-0.00280.09060.01610.0681-6.073-52.724-24.7184
80.3656-0.33520.04081.13810.64660.5712-0.0457-0.0732-0.10220.518-0.1265-0.06560.1928-0.10950.13290.2151-0.0853-0.04380.04080.03950.1313-16.3952-62.6381-21.8281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:113)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 114:204)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 205:296)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 297:331)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 22:119)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 120:209D)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 210A:297)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 298:331)

+
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://pdbjlvh1.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