[English] 日本語
Yorodumi
- PDB-9sc9: Crystal structure of Methanocaldococcus jannaschii Malate dehydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sc9
TitleCrystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant
ComponentsL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
KeywordsOXIDOREDUCTASE / Malate dehydrogenase / NADP binding domain
Function / homology
Function and homology information


L-2-hydroxycarboxylate dehydrogenase [NAD(P)+] / L-2-hydroxycarboxylate dehydrogenase (NAD+) activity / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
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
: / Chem-NDP / L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCoquille, S. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE44-0034-01 France
Agence Nationale de la Recherche (ANR)ANR-22-CE02-0027 France
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Unraveling the link between thermal adaptation and latent allostery in malate dehydrogenase from Methanococcales.
Authors: Pereira, C.S. / Coquille, S. / Brochier-Armanet, C. / Sterpone, F. / Madern, D.
History
DepositionAug 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
B: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
C: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
D: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,72516
Polymers140,2184
Non-polymers3,50612
Water00
1
A: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
C: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
hetero molecules

B: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
D: L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,72516
Polymers140,2184
Non-polymers3,50612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area20100 Å2
ΔGint-67 kcal/mol
Surface area42050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.992, 75.534, 118.502
Angle α, β, γ (deg.)90.000, 95.569, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) / MdhII


Mass: 35054.551 Da / Num. of mol.: 4
Mutation: P24S, E42K, E46M, R56G, P85A, K105N, D135E, K137G, R140K, K198R, T216G, K217Y, E219K, R223D, D266G, R277K, D289N, A295G, K305G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: mdh, mdhB, MJ0490
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q60176, L-2-hydroxycarboxylate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M potassium sodium tartrate, 0.1M BisTris propane pH 7.5, 16-18% PEG 3350 Cryo-protectant: 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.85→117.94 Å / Num. obs: 30234 / % possible obs: 98.6 % / Redundancy: 6.85 % / Biso Wilson estimate: 49.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.091 / Rrim(I) all: 0.231 / Net I/σ(I): 8.74
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 2.5 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 2216 / CC1/2: 0.424 / Rpim(I) all: 1.218 / Rrim(I) all: 2.7

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→117.94 Å / SU ML: 0.3517 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.7881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 1042 4.79 %
Rwork0.2049 20695 -
obs0.2068 21737 74.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.8 Å2
Refinement stepCycle: LAST / Resolution: 2.9→117.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9456 0 220 0 9676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00369796
X-RAY DIFFRACTIONf_angle_d0.576313214
X-RAY DIFFRACTIONf_chiral_restr0.04421555
X-RAY DIFFRACTIONf_plane_restr0.00471655
X-RAY DIFFRACTIONf_dihedral_angle_d16.04813686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.3686470.3181198X-RAY DIFFRACTION30.05
3.05-3.240.3325850.29321768X-RAY DIFFRACTION45.23
3.24-3.490.32911450.2612716X-RAY DIFFRACTION68.99
3.49-3.850.27752280.22813489X-RAY DIFFRACTION90.07
3.85-4.40.22751900.18583583X-RAY DIFFRACTION90.37
4.4-5.550.19731470.17523956X-RAY DIFFRACTION98.84
5.55-117.940.21282000.18393985X-RAY DIFFRACTION98.01
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)
13.3078943607-0.4276870341980.3932355291141.72332778269-0.5611570913071.67889898899-0.06752325370760.0637841392871-0.3755490120.08910890067610.209855902592-0.04201653450470.0372915915508-0.303755255069-0.0497552451210.222879121866-0.0288992515341-0.01219483232550.1876044945330.01523493773520.17581735692426.055564126811.441961945918.7296796052
22.61491883201-0.0736859092690.1574447396491.88898806558-0.5236688377620.613334792616-0.0981630243256-0.157396472612-0.608597132858-0.1382181421360.2068991296180.2441391066050.380692266827-0.2088126865970.04203669738930.351874701231-0.089367833808-0.01330337134170.2023550454950.02261703724470.3786799497120.8223437804-2.2749192228324.0758198446
31.367297235880.2729540195430.2739955088420.939630168998-0.3216004113530.946037972831-0.26887412939-0.9733993115650.04021978505790.4666777621690.05720367279410.07747319848160.336080391804-0.0480052959236-0.5826655062390.5044880699850.0974380484790.03990725220571.131350199850.143341880850.13956497651128.93736019446.6346069676351.0964861244
42.67999587483-1.05605231116-1.102049210242.674703122570.6306177332382.54925406539-0.33637238771-1.10917182672-0.04620592645720.4411684390760.2795078346730.02860872473340.0548001394869-0.259349471343-0.0590569553910.3199105305950.08091371500070.01454057288610.4969533095110.02928666035390.19959239280823.838813670910.264764030434.6166280808
50.5576061299690.0229189448952-0.4640505180270.606215327139-0.2885494639530.822443196006-0.225361651941-0.595009531958-0.5509220702710.3207074074580.1402799580980.01403363253250.15060968667-0.390304586735-0.02459013100590.3787882691010.126939800388-0.00731287698610.574286679450.4978265818930.5864865644831.0742312881-7.8602928019338.377058774
61.23906996754-0.38292697011-0.3135962972410.936843972311-0.3160338534861.3662498971-0.210446675903-0.744382763739-0.6368860338170.3516287841720.100870252710.1861146262720.701087750373-0.236025395783-0.06510510447420.584415604762-0.0734648769389-0.03426448436350.6316734852730.2688844735740.66777753763922.7748978832-10.386138945541.2043200244
73.79390441157-0.8154162795-0.786489196381.50072237185-0.3473161635712.591914789080.00867272104538-0.268929472925-0.1148648339250.00117237705156-0.24901064504-0.152716705239-0.3064763401220.225257811310.1111662384080.294907847623-0.00272725071450.01484399418670.2813063478160.03224486900870.185017127679-12.89478536817.0917283965125.4577191297
83.69300934198-0.4912197453440.8356155717190.5881028612290.5970828101451.1787553573-0.126990791645-0.931476387191-0.4635494627940.298541625083-0.1669682689740.04485051887490.241924488328-0.0290306258672-0.1063121417350.3518423076070.06701816573560.02096074692430.3557080000610.2704244532840.500186480556-13.45515086432.9320460064931.5016602214
92.895186099440.987992922530.02051450418560.453774209374-0.4703011087641.97888308464-0.445226811472-0.444136214836-0.974610610408-0.07806732390790.0694545492476-0.1286397064570.3206830327140.09829732503560.07791304251080.4531597520040.00784948277102-0.0264143067660.2230862106690.02927851410020.408981879366-14.7428652392-3.8315449559724.8048167219
103.702636072620.603659867454-0.1704048570171.62525814741-0.2823577438821.54380897236-0.004919452283840.154530799741-0.0155875788491-0.002779484737920.0186774604586-0.121777826914-0.0981721755936-0.0311632878297-0.001604452758550.221623990538-0.02136779242990.03359232564130.267777445387-0.07713397523840.265261088951-3.220702884076.101044708613.5220960207
113.62270292876-0.232669719123-0.1239699073113.088624373390.4813430130312.340395869060.132206736741.07055629786-0.195847978999-0.133955236399-0.1102344928290.01129147845720.5025261715190.2521311974020.01416137420170.3339786487860.04798897693730.007136952662150.504410475246-0.05094485044640.232297633921-10.5304792876.885736202456.76658831432
120.475139256060.103720488052-0.3426602894121.16457307852-0.04915141328471.077889373890.1239899907130.08221814766530.98748552391-0.1851235878940.0410277473305-0.0107116373917-0.192887844474-0.00671356774561-0.0810183739890.419135385522-0.1002587855730.02318561725150.2206581894230.01054189161290.714222928585-17.390296405632.23280904712.9879712056
132.71724290416-1.02757483263-0.1799918770833.45911960392-1.390575416573.94887432488-0.295163260676-0.004651671258311.044070992210.09678517012510.137571291392-0.576333934904-0.6312894882880.589697718142-0.02990198257810.394108844413-0.166722938290.1328925508570.307462575532-0.07429759850630.694259006936-4.0826153374430.347033740318.152429048
143.82081530942-0.65416708659-0.03963309617051.79864087495-0.2759864097572.1070657360.1400772390650.8360283070420.351566922589-0.404317439107-0.138441540079-0.111547492876-0.1297207040720.0167370448468-0.03052867289390.279451827825-0.02590334426530.009510085801880.302945329627-0.01238936052080.254571949241-14.146649838816.26223674976.22445794315
151.839869378930.234461646762-1.030026278992.604089959070.02832512767031.249904157780.216796528092-0.7730179820660.961677524770.1068573144890.08621626734030.163963548854-0.317869112597-0.0647528507354-0.1005857040530.3179428048070.09632715728880.01104294669490.415026596616-0.2132654507820.54111603786123.321904308832.106430273234.2753451143
162.156886273520.103394500066-0.1348960500040.45032752560.04806847261440.9824780690620.1807621271510.5544905864141.46024915886-0.1629291673010.1471537479110.0607409365867-0.349769655584-0.186033835027-0.05670998460540.4276388002210.04342022018970.0512909478390.1024834729060.06559915114780.84765519837133.50947588536.205709972914.6127552543
171.9293444732-0.05028140416840.0196431077895.21159115753-0.3165828212281.02673860825-0.356534303183-1.137452333470.6720704833720.2698687195910.179861291627-0.811580306168-0.437920497545-0.0965362193721-0.3992414878070.271608798891-0.00903086952219-0.1428509194090.652323363095-0.2143737230660.274343551124-13.236907092623.273135247639.2770218816
180.819593303493-0.245513675808-0.1675789125872.70420948974-0.221414906580.98258702763-0.121224276438-0.7967224778480.937567354910.181007967743-0.0236383103187-0.303556373861-0.1785308228510.287610587290.03285748351070.377581370948-0.0790733881083-0.0699010814770.496121381195-0.2119914914980.530360482654-11.257726045927.517932298433.6195000063
190.3274854063160.2896405306390.2287874427611.060096024060.1249254465980.5973988406250.0497885472899-0.9539383074420.5597044845730.285103827027-0.0718526312105-0.283923854431-0.3322623351580.1535141803280.3489328940830.454440595143-0.0677547688871-0.1921166700081.25113300419-0.5363399706230.588146319548-11.569249204726.326056369751.1055516769
200.456870695275-0.418203707161-0.6551748266631.646243344920.5706111382411.480031430210.0577952997576-0.967553224045-0.1123198941590.5234485715190.5769641972920.1002994083660.07812673127680.2204457700120.6210015632050.4705634591940.13732968147-0.01392380960141.177954676960.2964853100030.25526070428-24.3358212611.6047049609649.5736801739
213.06938724422-0.935821711266-0.01334469717720.8550743557090.4070315161320.2855028686460.128187341887-0.764305489942-0.9865979324760.268029283628-0.1615749169440.1077517360830.0560096271636-0.167076788222-0.3786942432240.4898367895710.122778608415-0.09263753672931.083830586030.377872663050.511242085029-21.3838960139-8.2469638262950.5895270086
222.46005007383-0.740863577069-0.02866079865871.993746257850.3431782634050.742043289803-0.451183792575-1.02135613356-0.2824573627090.2236638268820.4060147158910.1085940163710.0505976942412-0.08948764729620.01000647559030.359407452042-0.0047172078255-0.05426845027070.660602944966-0.0112411048140.44408493023-14.174051758911.575328670742.4388076936
231.08355064515-0.3148169002310.8775529773580.0872010052664-0.2451413463830.714874090752-0.15469377615-1.20008898352-0.009458150311380.4601117170030.0233740785522-0.189601756437-0.03280530450660.1683244665350.007669870557380.5998661153310.144852774659-0.05860902462591.6276915739-0.106539572350.300846117414-23.353122810213.671355714460.7767966019
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 54 )AA1 - 541 - 54
22chain 'A' and (resid 55 through 148 )AA55 - 14855 - 148
33chain 'A' and (resid 149 through 215 )AA149 - 215149 - 215
44chain 'A' and (resid 216 through 244 )AA216 - 244216 - 244
55chain 'A' and (resid 245 through 275 )AA245 - 275245 - 275
66chain 'A' and (resid 276 through 314 )AA276 - 314276 - 314
77chain 'B' and (resid 1 through 21 )BD1 - 211 - 21
88chain 'B' and (resid 22 through 55 )BD22 - 5522 - 55
99chain 'B' and (resid 56 through 76 )BD56 - 7656 - 76
1010chain 'B' and (resid 77 through 124 )BD77 - 12477 - 124
1111chain 'B' and (resid 125 through 148 )BD125 - 148125 - 148
1212chain 'B' and (resid 149 through 206 )BD149 - 206149 - 206
1313chain 'B' and (resid 207 through 224 )BD207 - 224207 - 224
1414chain 'B' and (resid 225 through 313 )BD225 - 313225 - 313
1515chain 'C' and (resid 1 through 124 )CG1 - 1241 - 124
1616chain 'C' and (resid 125 through 313 )CG125 - 313125 - 313
1717chain 'D' and (resid 1 through 21 )DJ1 - 211 - 21
1818chain 'D' and (resid 22 through 54 )DJ22 - 5422 - 54
1919chain 'D' and (resid 55 through 148 )DJ55 - 14855 - 143
2020chain 'D' and (resid 149 through 198 )DJ149 - 198144 - 193
2121chain 'D' and (resid 199 through 215 )DJ199 - 215194 - 210
2222chain 'D' and (resid 216 through 244 )DJ216 - 244211 - 239
2323chain 'D' and (resid 245 through 307 )DJ245 - 307240 - 302

+
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