[English] 日本語
Yorodumi
- PDB-8ab3: Crystal Structure of the Lactate Dehydrogenase of Cyanobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ab3
TitleCrystal Structure of the Lactate Dehydrogenase of Cyanobacterium Aponinum in complex with oxamate, NADH and FBP.
ComponentsL-lactate dehydrogenase
KeywordsOXIDOREDUCTASE / allostery / lactate dehydrogenase / crystallophore / XO4
Function / homology
Function and homology information


L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / 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 domain superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / OXAMIC ACID / L-lactate dehydrogenase
Similarity search - Component
Biological speciesCyanobacterium aponinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.616 Å
AuthorsRobin, A.Y. / Girard, E. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Other governmentprogram CrysFrag R&D booster region AuRA France
Other governmentProgram XO4_2.0 Pack ambition recherche region AuRA France
CitationJournal: Mol.Biol.Evol. / Year: 2023
Title: Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery.
Authors: Robin, A.Y. / Brochier-Armanet, C. / Bertrand, Q. / Barette, C. / Girard, E. / Madern, D.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-lactate dehydrogenase
B: L-lactate dehydrogenase
C: L-lactate dehydrogenase
D: L-lactate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,84114
Polymers148,1434
Non-polymers3,69810
Water8,845491
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SEC-malls performed before addition of 3 ligands for co-crystallization experiment., light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29110 Å2
ΔGint-178 kcal/mol
Surface area42480 Å2
Unit cell
Length a, b, c (Å)70.369, 111.504, 101.793
Angle α, β, γ (deg.)90, 99.78, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
L-lactate dehydrogenase / L-LDH


Mass: 37035.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The four chains of this entry are identical and correspond to the the entered sequence. The sequence is the one of C.aponinum LDH with a fixed 6 histidine tag in Cterminus. For chains A and ...Details: The four chains of this entry are identical and correspond to the the entered sequence. The sequence is the one of C.aponinum LDH with a fixed 6 histidine tag in Cterminus. For chains A and C, there is no electronic density for the last residue and the histag.
Source: (gene. exp.) Cyanobacterium aponinum (bacteria) / Strain: PCC 10605 / Gene: ldh, Cyan10605_1816 / Production host: Escherichia coli (E. coli) / References: UniProt: K9Z684, L-lactate dehydrogenase
#2: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18.5 % peg 3350 0.24 M sodium malonate dibasic monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.616→100.314 Å / Num. obs: 46537 / % possible obs: 99.3 % / Redundancy: 4.31 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.983 / CC1/2 anomalous: -0.127 / Rmerge(I) obs: 0.1946 / Rpim(I) all: 0.105 / Rrim(I) all: 0.222 / AbsDiff over sigma anomalous: 0.745 / Net I/σ(I): 5.62 / Num. measured all: 200506 / % possible anomalous: 95.8 / Redundancy anomalous: 2.23
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
7.1-100.3144.030.080911.2993689368232423240.991-0.3710.04460.09290.584942.1396.1
5.636-7.14.050.12078.6495309530235523550.981-0.1080.06750.1390.69295.32.1299.5
4.923-5.6363.880.12588.0290449044233323330.983-0.0950.07150.14530.72593.22.0498.9
4.473-4.9234.010.12478.993399339233123310.98-0.160.07010.14370.7496.52.0699.1
4.153-4.4734.110.12358.9794729472230723070.98-0.0860.06860.14190.7596.82.1199.2
3.908-4.1534.180.13598.3496669666231423140.981-0.0990.07490.15580.78996.42.1598.9
3.712-3.9084.230.1477897919791231623160.98-0.1750.08060.16880.75595.72.1898.9
3.55-3.7124.310.18416.941005510055233423340.972-0.070.09980.21020.79896.32.2299.2
3.414-3.554.290.20736.1999969996232823280.966-0.0680.11140.23610.76695.52.2399.4
3.296-3.4144.320.24255.531008110081233423340.962-0.0730.13020.27610.79395.32.2499.5
3.193-3.2964.350.27484.81005210052230923090.952-0.0950.14610.31230.76194.32.2799.3
3.102-3.1934.390.32054.311023210232233123310.943-0.0650.16940.36380.77194.62.2999.8
3.02-3.1024.430.37943.761031110311233023300.916-0.0790.20010.43050.77295.62.399.7
2.946-3.024.480.41643.491028010280229722970.883-0.0770.21880.47190.76395.92.3299.7
2.879-2.9464.480.43613.281059410594236523650.909-0.0790.22830.49390.73895.92.3299.7
2.818-2.8794.510.48582.91037510375229922990.892-0.0220.25370.54980.74996.72.3299.7
2.762-2.8184.510.55892.621048810488232723270.846-0.0880.29270.6330.75396.22.3399.8
2.71-2.7624.570.63552.361065710657233123310.794-0.0480.330.71820.73996.52.3599.7
2.661-2.714.510.67692.181050010500233023300.749-0.0670.35290.76580.72396.52.3399.9
2.616-2.6614.560.75441.991067510675234223420.726-0.030.39140.85250.731982.33100

-
Processing

Software
NameVersionClassification
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022data reduction
Aimless0.7.4data scaling
TRUNCATE7.1.011data processing
BUSTER2.10.4 (8-JUN-2022)refinement
BUSTER2.10.4 (8-JUN-2022)refinement
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ojn

4ojn


Resolution: 2.616→100.31 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.803 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.832 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2317 -RANDOM
Rwork0.1862 ---
obs0.1884 46528 99.3 %-
Displacement parametersBiso mean: 39.64 Å2
Baniso -1Baniso -2Baniso -3
1-15.5699 Å20 Å20.3017 Å2
2---8.3056 Å20 Å2
3----7.2643 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.616→100.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9900 0 240 491 10631
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710326HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9314070HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3636SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1788HARMONIC5
X-RAY DIFFRACTIONt_it10326HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1492SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8145SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion17.55
LS refinement shellResolution: 2.62→2.63 Å
RfactorNum. reflection% reflection
Rfree0.3712 51 -
Rwork0.2444 --
obs0.2514 931 100 %
Refinement TLS params.

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)
11.04690.0071-0.23660.19620.06660.3663-0.018-0.0081-0.0032-0.00810.0348-0.0386-0.0032-0.0386-0.0169-0.04860.0069-0.0214-0.11350.05530.0963-44.9073-3.5494-16.5158
20.74570.1155-0.02060.2515-0.05680.46780.0051-0.0167-0.0107-0.01670.01260.0981-0.01070.0981-0.0177-0.05080.01020.0101-0.0796-0.0740.0833-15.756615.5827-7.0299
30.9576-0.1132-0.06270.1079-0.30850.44250.03690.0007-0.01160.0007-0.01090.0509-0.01160.0509-0.026-0.02640.0035-0.0278-0.1157-0.05190.0742-11.07991.8561-36.5737
40.87930.1006-0.00990.1538-0.08190.6198-0.01040.0381-0.08270.03810.0529-0.0588-0.0827-0.0588-0.0425-0.0390.0164-0.0113-0.14450.06030.1344-40.891322.5891-36.4415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 332
2X-RAY DIFFRACTION1{ A|* }A401
3X-RAY DIFFRACTION2{ B|* }B3 - 330
4X-RAY DIFFRACTION2{ B|* }B401
5X-RAY DIFFRACTION3{ C|* }C3 - 332
6X-RAY DIFFRACTION3{ C|* }C401
7X-RAY DIFFRACTION4{ D|* }D4 - 331
8X-RAY DIFFRACTION4{ D|* }D401

+
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