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- PDB-9end: Crystal structure of Methanopyrus kandleri malate dehydrogenase m... -

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Basic information

Entry
Database: PDB / ID: 9end
TitleCrystal structure of Methanopyrus kandleri malate dehydrogenase mutant 3
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / Rossmann-like motif / NAD(P)H binding site
Function / homology
Function and homology information


lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process
Similarity search - Function
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
Chem-NDP / Malate dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCoquille, S. / Roche, J. / Girard, E. / Madern, D.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-16-CE11-0011 France
Agence Nationale de la Recherche (ANR)ANR-21-CE44-0034-01 France
CitationJournal: To be published
Title: Navigating the conformational landscape of an enzyme. Stabilization of a low populated conformer by evolutionary mutations triggers Allostery into a non-allosteric enzyme.
Authors: Coquille, S. / Simoes Pereira, C. / Brochier-Armanet, C. / Roche, J. / Santoni, G. / Coquelle, N. / Girard, E. / Sterpone, F. / Madern, D.
History
DepositionMar 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9867
Polymers69,4142
Non-polymers1,5725
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, homology, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-62 kcal/mol
Surface area22910 Å2
Unit cell
Length a, b, c (Å)78.820, 78.820, 251.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-569-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 34706.980 Da / Num. of mol.: 2 / Mutation: D51H, R85Q, K156R, S228T, P232I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: HA336_00525 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A832T926
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium citrate tribasic monohydrate, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 58752 / % possible obs: 99.7 % / Redundancy: 7.75 % / Biso Wilson estimate: 40.38 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.93
Reflection shellResolution: 1.95→2 Å / Redundancy: 8.18 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4274 / CC1/2: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.78 Å / SU ML: 0.2143 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.8118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 2938 5 %
Rwork0.1949 55801 -
obs0.1967 58739 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.67 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 99 256 4874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00974721
X-RAY DIFFRACTIONf_angle_d1.04816426
X-RAY DIFFRACTIONf_chiral_restr0.0527789
X-RAY DIFFRACTIONf_plane_restr0.0089819
X-RAY DIFFRACTIONf_dihedral_angle_d14.85171729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.3341390.29272625X-RAY DIFFRACTION99.93
1.98-2.020.31041360.27152587X-RAY DIFFRACTION100
2.02-2.050.30731370.25922616X-RAY DIFFRACTION100
2.05-2.090.26361380.23942617X-RAY DIFFRACTION100
2.09-2.130.26991380.24122624X-RAY DIFFRACTION99.89
2.13-2.180.26461380.21962618X-RAY DIFFRACTION99.82
2.18-2.230.25481380.21382619X-RAY DIFFRACTION99.96
2.23-2.290.20431380.19312614X-RAY DIFFRACTION100
2.29-2.350.24871380.19262641X-RAY DIFFRACTION100
2.35-2.420.24351390.18782636X-RAY DIFFRACTION100
2.42-2.50.21521380.19212620X-RAY DIFFRACTION99.86
2.5-2.590.22421390.20042638X-RAY DIFFRACTION99.96
2.59-2.690.22271390.19742638X-RAY DIFFRACTION100
2.69-2.810.27061400.20242667X-RAY DIFFRACTION99.96
2.81-2.960.26451400.21332664X-RAY DIFFRACTION99.93
2.96-3.140.27171390.20792637X-RAY DIFFRACTION98.68
3.14-3.380.241390.19362646X-RAY DIFFRACTION98.72
3.38-3.720.19441420.18222699X-RAY DIFFRACTION99.82
3.72-4.260.20551430.15692709X-RAY DIFFRACTION99.89
4.26-5.340.18431460.15712770X-RAY DIFFRACTION99.97
5.35-19.780.24721540.22892916X-RAY DIFFRACTION99.45
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)
11.96929065457-0.05241013707011.111984699643.48140073275-0.3867857706182.30932662551-0.137486049558-0.09590558092470.0172889844780.003042743087760.2268754538610.2446896236-0.190306400792-0.214310052277-0.04948529195530.4509412472250.04919064144960.009222675779860.305522921474-0.008629223825650.276095850271.49542883855-11.981148372943.6979190684
26.130507911690.718037007312-3.38175222764.09827884294-0.4959864344625.53939360292-0.302371601060.7087640468210.19619533775-1.364200745450.0351229771899-0.158648223087-0.1454055938-0.4480834376040.1995031985010.87917216331-0.0177835001032-0.01856995923330.423869277270.03937061754930.4031070714097.374595386421.6527122080628.687230192
32.23789341950.624684305551-0.7860871537292.68638210538-0.2363319685372.11326784855-0.1765122553490.100990610020.287112045909-0.06188813767820.04028325031820.172224898041-0.383042479903-0.318684144940.1686473237780.7132511671430.12253676605-0.08517874298890.280952900471-0.01311307834210.4209736085776.334225062536.0008302245141.1515677512
41.573070265640.6391698234070.319316907952.44837210418-1.178150069882.27016098732-0.06743021142960.2284304483130.0518656637007-0.627407816893-0.104041814656-0.651553506667-0.07657369675690.6275788563470.1587223379790.564688285467-0.03258900011330.1148233607760.3866473891240.008079276726760.58175547513931.8774144674-3.7311473464645.4295045299
51.481205634660.5854734830740.1124387296012.61387165381-0.9171973418961.54409216878-0.176112669579-0.1780372942360.3777843642190.2698085381880.0890649620263-0.436818428176-0.4830171151470.1150858618320.04774604849840.6700838800090.0421843932952-0.104657997170.291592537329-0.06802900316270.43933307733416.23518205644.3014764417148.5281732985
64.90589079924-0.2107540731861.526049315672.70545140610.8066178153333.127599888450.02909929320911.010577437770.720490869467-1.29893732753-0.240397660748-0.774168970663-0.5873819432090.4963981940720.1580376074781.16561262911-0.005505002951230.06845723798780.343984445790.1206474577580.71979951314521.86255641412.475807445433.9512671534
71.689193483170.212767333346-0.05764031420863.61777464989-0.2485453547021.734279431870.01082486006580.0932300063182-0.124023623857-0.2942721790310.0336554010259-0.1616376830470.2865274262560.0696030121709-0.0537693283610.4273793773270.02590491818690.010061320160.236823757986-0.0262500037760.3017475630122.2114184056-32.477459806244.8388647081
82.15616330686-0.1918690712240.06766132128622.78752116062-0.4641519618781.31402632376-0.0490718577375-0.1644747942630.653676959391-0.08407829320640.1144149851790.494569248325-0.575623802623-0.514514009167-0.1490976270870.5904352380370.007240496200270.01814657427660.5645434775790.08717525330270.853200972729-3.50883535724-32.314962701553.6233136241
91.46135883370.2263570102710.1496283079592.127320401991.09728460191.454023328430.0479809804692-0.188853943339-0.2774509298690.206513537818-0.0414359444020.1644618506660.42888386971-0.159228589658-0.03237283043560.493684471846-0.0534948920978-0.003588810004760.2894886579220.03985562738070.37926316214211.0627738855-37.990726778856.9994038596
104.6808571475-1.10691271479-2.6722436922.599840034230.6131390659325.01932447449-0.1052361273220.656708124574-0.879660023736-0.4702383092950.01286884749770.4043011939151.25705762709-0.7783702454260.1607445813950.756371212947-0.190689585246-0.08746740422130.323533339636-0.01346008039250.6462152248234.6286862332-51.304398285947.5922344025
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 90 )AA2 - 901 - 83
22chain 'A' and (resid 91 through 106 )AA91 - 10684 - 99
33chain 'A' and (resid 107 through 148 )AA107 - 148100 - 141
44chain 'A' and (resid 149 through 224 )AA149 - 224142 - 217
55chain 'A' and (resid 225 through 289 )AA225 - 289218 - 282
66chain 'A' and (resid 290 through 314 )AA290 - 314283 - 307
77chain 'B' and (resid 2 through 147 )BC2 - 1471 - 140
88chain 'B' and (resid 148 through 222 )BC148 - 222141 - 206
99chain 'B' and (resid 223 through 289 )BC223 - 289207 - 271
1010chain 'B' and (resid 290 through 315 )BC290 - 315272 - 297

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