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- PDB-9sa7: Crystal structure of Methanocaldococcus jannaschii Malate dehydro... -

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Basic information

Entry
Database: PDB / ID: 9sa7
TitleCrystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7 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 speciesMethanocaldococcaceae (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,1828
Polymers138,2014
Non-polymers2,9824
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14860 Å2
ΔGint-51 kcal/mol
Surface area47170 Å2
Unit cell
Length a, b, c (Å)87.764, 87.764, 338.338
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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


Mass: 34550.133 Da / Num. of mol.: 4
Mutation: E42K, E46M, K105N, D135E, R140K, K198R, K217Y, E219K, R223D, R278K, D250N, K306G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcaceae (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
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 % / Description: Pyramidal shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 19-29 % Ethylene glycol Cryogenic conditions: 35% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.8→169.17 Å / Num. obs: 34675 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 72.14 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.08 / Rrim(I) all: 0.17 / Net I/σ(I): 4.3
Reflection shellResolution: 2.8→2.945 Å / Rmerge(I) obs: 1.547 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1704 / CC1/2: 0.392 / Rpim(I) all: 0.843 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→112.78 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2464 1581 4.8 %
Rwork0.2152 31337 -
obs0.2167 32918 85.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.58 Å2
Refinement stepCycle: LAST / Resolution: 2.8→112.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9474 0 192 0 9666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00759798
X-RAY DIFFRACTIONf_angle_d0.817813243
X-RAY DIFFRACTIONf_chiral_restr0.0481573
X-RAY DIFFRACTIONf_plane_restr0.00421660
X-RAY DIFFRACTIONf_dihedral_angle_d15.13913710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.4395430.3548886X-RAY DIFFRACTION27.17
2.89-2.990.3112660.30661406X-RAY DIFFRACTION42.99
2.99-3.110.33451300.31412489X-RAY DIFFRACTION76
3.11-3.260.33431680.30833265X-RAY DIFFRACTION99.56
3.26-3.430.35921330.29483273X-RAY DIFFRACTION99.21
3.43-3.640.30311810.25893267X-RAY DIFFRACTION98.94
3.64-3.920.26721900.23583232X-RAY DIFFRACTION99.65
3.92-4.320.24621530.20863335X-RAY DIFFRACTION99.66
4.32-4.940.18621500.17353358X-RAY DIFFRACTION99.4
4.94-6.230.22141780.19613347X-RAY DIFFRACTION99.16
6.23-112.780.19821890.16593479X-RAY DIFFRACTION97.27
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)
12.27991163483-0.294798323961-0.6391334602732.43386505692-0.4690920241572.404273873970.1433985900110.323547360253-0.218091820315-0.1276548459110.1755715908270.4249796265270.272914749012-0.490364633676-0.316538202350.420391138173-0.031820343463-0.100585112420.451404992130.0350351203480.598321032651-44.045210491514.067020918134.4751023549
21.816267644930.605771009251-0.1639411469692.26379579423-0.6552704356790.6287586387710.09121913097330.230093743274-0.317789356121-0.38557311526-0.001857513585920.2059212831330.4507154468890.0222140462288-0.08046933491770.6492968138720.0265223142539-0.09542050578860.288088049544-0.05307155474540.429927074246-29.85728154410.27179336979437.0957543367
31.533632961020.2642746997350.01693142551442.00459511237-0.3641927144711.54050164349-0.0542964730340.208663275742-0.314674223796-0.252551414375-0.0840367500946-0.1136286251230.3525306362980.2722757070560.1378323805990.6113497463920.105138186592-0.01980307985750.350946765852-0.06187602407930.424138196708-17.68098854453.1632586447436.3633721522
44.417554021350.319487826466-0.7685004619641.84297095096-0.5565808979083.050950233280.06985493532960.610198618363-0.825681119548-0.681728451333-0.08283039488-0.5606999710980.8095084420720.1977600830220.01689787590390.8740293505780.1752285830460.01470079962560.393239265499-0.04270018893340.703387245201-21.3897410122-12.927693574540.0529017592
51.32910689271-1.638608118040.2186160637233.0659857585-0.3898503104082.74023615052-0.340386351534-0.2590849035060.1151474147530.9577340102920.06789462676810.0286703768905-0.155907735690.1713892846220.2787120377070.71657808914-0.00498905908935-0.08086542902270.2902506194110.00287202215260.404321523865-27.721078927827.008551927852.6178396915
62.14447827077-0.6026529190070.9047188431343.37541384181-0.324734960682.83451596113-0.252933473919-0.170424713840.4330809520470.8511324830050.2909240194320.420868782327-0.730165981743-0.494739402534-0.02549504440340.7074769282280.1181978524570.09627761980610.3049173336020.02585269718020.61771874557-44.165178470841.660880638345.0457637743
74.003381689290.3932853777150.06286471949673.269642498760.1356108794423.072458085590.1857327092620.3467069666790.2300431045050.180480982853-0.306153561661-0.355049180695-0.8936895982741.36346188760.1409023408330.59743968589-0.2587729267270.03734119092170.705060679210.02424884420180.5079946352-9.3908576203139.314401222820.8139476203
81.31855185893-0.225568544309-0.2675629755191.06211077281-0.6434982008690.794620048149-0.3178537469210.332937145240.806164379947-0.3158179659890.17269985227-0.353400984994-0.270471004870.4999129162280.2148161034720.92795267941-0.337955462997-0.0166672639630.6772970129020.06843098316070.718701974415-12.220352341546.258713911920.0252498669
91.34645816484-0.5339228460160.6830623409111.43439904388-0.6502214172080.5407162100320.2783601196940.4624146954350.321234376813-0.106179706135-0.118523039419-0.728260662161-0.7636325894050.649529818023-0.03916012027650.887395501638-0.4440341274030.03803493683620.9836892056850.03047814279210.8474092774440.2083206136943.110123916721.6786269063
101.22206437668-0.007050282350630.2938597346090.166715384783-0.1545575514260.1607894847880.05286849389330.3412213775490.7014484679980.123101541942-0.259596595216-0.609813952011-0.6550257946210.8396173252640.2591164273780.605997930672-0.347511798149-0.02730242783690.9683267896970.1646767195651.037257848386.806605349134.768156575623.8562001084
111.583690859010.2403780668150.4838536082882.66645434655-0.4898869118731.721213679010.01819588355210.50524311652-0.3137079442160.1133541934730.0553333065927-0.4144870812870.2978132549190.847349727269-0.04496068261580.5945125034110.03143276471790.1394212429440.684493040659-0.04153351292450.600590538915-2.8194095391416.8244393221.7818936028
122.098305016470.1925870718110.6677606418421.29687241121.116094852791.25234583821-0.1351219555540.63358214204-0.368449767542-0.1078024049170.247877934306-0.2735671537060.5035542225180.372668107487-0.1445115937250.9617474038430.0499238262480.1430539083660.966059408611-0.1694782073590.697749979508-4.4905702646713.537395015210.3982599194
132.292503337380.09302755063680.7638500182812.238113014820.3425967475061.999648203520.009078647685160.113724876433-0.04223332820190.403473504579-0.120125497156-0.622499868265-0.0008110068348110.9355031330180.1351252001810.623580210722-0.109355846269-0.05994657617830.7904228739590.07978415378160.6221676359910.63160457585723.917251224629.3059205026
140.3146418065680.525710672940.2310421156860.9260520723550.4157673237882.144028009870.05552621372681.26628018124-0.445624399180.259497450195-0.117286988019-0.2988963715120.7892949069121.56783577974-0.1712351873240.5764410213060.2107478858420.2855941157261.432615531630.1412418353091.2112499129814.010122717116.181121929219.0447260623
153.98070327975-0.1385099743640.1184514293993.752291853980.5720587499843.87438863738-0.1512201320221.06802895085-0.0781433071801-0.48251762129-0.1594576409380.3275650961530.132676704149-0.2491267958750.2813167131690.684616778708-0.220251333969-0.03361579699830.62465230725-0.01526890180480.410355038127-23.909663421731.02139053867.31214053814
161.5786044813-1.1686123136-0.1273997223961.67835231459-0.4067307136751.97860355673-0.009836772533250.387462212392-0.102662248439-0.590440393553-0.194814845190.1980589986620.1748931817030.3423873165460.2361782587120.888048735828-0.1940175953230.04422769067550.799617345448-0.1226770363560.52122713088-22.465069617826.46260507913.01911056079
174.94401624832-0.731637218792-0.214496586560.219654787804-0.4415295014181.680044113880.7987285618072.06485056316-0.108717464371-0.246689561151-0.328469205245-0.206136720439-0.280314710034-1.13230878411-0.3586627162061.28894816559-0.0641374376814-0.1084853826551.351816591780.1362596465060.506542525947-31.413392982939.4537235801-8.22408213185
181.15050397575-0.7629741562570.2535247634230.394358003113-0.1675601384361.05472362101-0.2309519861840.959974907162-0.0633912054543-0.518992770389-0.05997619670630.309939900103-0.333023198571-0.2325887622690.258208842920.94726370532-0.233964409223-0.3070124329051.011952141250.03581100589920.626367843398-36.486701351138.3378293814-1.48775134445
192.26311131642-0.8607037066840.233159513210.986315969085-0.2883011762331.286720640140.2788456478450.2705090468460.2532369465330.445880527716-0.0837529560790.170637991602-0.467071552176-0.304855691808-0.3743579815010.953087631151-0.183656021942-0.09792980784350.520858838340.1604014916890.540409551365-35.982425822744.542178339612.9575716342
201.20892952254-0.568786703591.180940117360.919052880961-0.5599425942681.35411352822-0.1096973427460.1003275972940.547414948223-0.1505962033090.1596800116120.320009785311-1.16887169793-0.02898386306850.01144225160591.1064118282-0.0246743395257-0.1941946887710.5770579909920.1535629099110.786789905193-35.271076839454.703109873419.9611001639
210.905999662445-0.46293334362-0.183263511.672120244560.6760829019361.83202360621-0.180193221980.909839325797-0.0932291074371-0.311562952774-0.03788961584350.357500302622-0.232650607567-0.1286303357820.1336223913250.685826175634-0.229973689792-0.1780414455570.7377268047080.08801453449180.617975276374-37.4351830440.985508603510.0942332607
223.489373310990.3472693071170.05899739461273.7855290823-1.015375894743.467019792540.1832090243690.592142577084-0.6325905453790.005248445997080.1912008767380.927148460484-0.142083285465-0.457063806897-0.4628995470220.692823708014-0.158228906743-0.2411317706110.8759201832650.1094689102990.801435152247-47.725496081841.126906760312.3313642402
230.5045564819070.093897385021-0.5091478908710.4767811452160.656855339531.11905685378-0.6089558610260.6793889111620.779218912892-0.541020649469-0.008172982697260.160933691517-1.12783920192-0.7105651321370.4388258699921.483891945920.0456812952861-0.3675053514961.196004806460.4198267264221.01223624023-42.604997047853.5835137036-0.930454190871
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 72 )AA1 - 721 - 72
22chain 'A' and (resid 73 through 179 )AA73 - 17973 - 179
33chain 'A' and (resid 180 through 289 )AA180 - 289180 - 289
44chain 'A' and (resid 290 through 312 )AA290 - 312290 - 312
55chain 'B' and (resid 1 through 91 )BC1 - 911 - 91
66chain 'B' and (resid 92 through 313 )BC92 - 31392 - 313
77chain 'D' and (resid 1 through 22 )DE1 - 221 - 22
88chain 'D' and (resid 23 through 52 )DE23 - 5223 - 52
99chain 'D' and (resid 53 through 113 )DE53 - 11353 - 109
1010chain 'D' and (resid 114 through 136 )DE114 - 136110 - 132
1111chain 'D' and (resid 137 through 195 )DE137 - 195133 - 191
1212chain 'D' and (resid 196 through 229 )DE196 - 229192 - 225
1313chain 'D' and (resid 230 through 289 )DE230 - 289226 - 282
1414chain 'D' and (resid 290 through 306 )DE290 - 306283 - 299
1515chain 'C' and (resid 1 through 22 )CG1 - 221 - 22
1616chain 'C' and (resid 23 through 91 )CG23 - 9123 - 87
1717chain 'C' and (resid 92 through 113 )CG92 - 11388 - 109
1818chain 'C' and (resid 114 through 136 )CG114 - 136110 - 132
1919chain 'C' and (resid 137 through 163 )CG137 - 163133 - 159
2020chain 'C' and (resid 164 through 222 )CG164 - 222160 - 218
2121chain 'C' and (resid 223 through 274 )CG223 - 274219 - 270
2222chain 'C' and (resid 275 through 289 )CG275 - 289271 - 285
2323chain 'C' and (resid 290 through 313 )CG290 - 313286 - 309

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