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- PDB-8rwl: Crystal structure of Methanopyrus kandleri malate dehydrogenase m... -

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Basic information

Entry
Database: PDB / ID: 8rwl
TitleCrystal structure of Methanopyrus kandleri malate dehydrogenase mutant 1
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / Rossmann-like motif / NAD(P)H binding site
Function / homology
Function and homology information


malate dehydrogenase [NAD(P)+] / L-malate dehydrogenase (NADP+) activity / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle
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 / Malate dehydrogenase
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCoquille, S. / Roche, J. / Engilberge, S. / 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
DepositionFeb 5, 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)71,26313
Polymers69,2522
Non-polymers2,01211
Water2,558142
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,52626
Polymers138,5034
Non-polymers4,02322
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)78.250, 78.250, 251.300
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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malate dehydrogenase


Mass: 34625.836 Da / Num. of mol.: 2 / Mutation: R85Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: mdh, MK1069 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TWG5, malate dehydrogenase [NAD(P)+]

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Non-polymers , 5 types, 153 molecules

#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-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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 10 mM Hepes pH 7.5, 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 35833 / % possible obs: 99.9 % / Redundancy: 18.25 % / Biso Wilson estimate: 55.33 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.064 / Net I/σ(I): 27.84
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2568 / CC1/2: 0.578 / Rrim(I) all: 1.113

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.92 Å / SU ML: 0.2617 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0945
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2429 1782 5 %
Rwork0.2044 33871 -
obs0.2064 35653 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 125 142 4777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00964678
X-RAY DIFFRACTIONf_angle_d0.99826355
X-RAY DIFFRACTIONf_chiral_restr0.0538783
X-RAY DIFFRACTIONf_plane_restr0.0071806
X-RAY DIFFRACTIONf_dihedral_angle_d16.32691711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.30781310.28322515X-RAY DIFFRACTION99.14
2.36-2.430.28451340.25852556X-RAY DIFFRACTION100
2.43-2.510.32821340.24672544X-RAY DIFFRACTION100
2.51-2.60.29441350.22872556X-RAY DIFFRACTION99.96
2.6-2.70.27541360.21632575X-RAY DIFFRACTION99.93
2.7-2.830.27711350.21792564X-RAY DIFFRACTION99.89
2.83-2.970.25691350.23382577X-RAY DIFFRACTION100
2.97-3.160.26261370.21312595X-RAY DIFFRACTION100
3.16-3.40.25481370.20912612X-RAY DIFFRACTION99.96
3.4-3.740.24441380.19762620X-RAY DIFFRACTION100
3.74-4.280.20821380.17822628X-RAY DIFFRACTION100
4.28-5.370.21341420.1722687X-RAY DIFFRACTION100
5.38-19.920.24271500.21942842X-RAY DIFFRACTION99.97
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)
16.48229082669-1.23508298855-1.422739294122.36705475863-0.05807850538032.98874228963-0.09678527027760.7949059417890.46259273917-0.198177947976-0.0971985352048-0.256823778692-0.5281459590190.6303393883560.1495367661210.429693177221-0.185659881442-0.08346775185720.7356285093180.137166907410.445601049078-4.8220481761-3.02203890381-22.5595275386
24.92443699307-0.321659626253-1.204262495773.0506027947-1.322507170785.63986719345-0.1474483265270.538538712154-0.568066842088-0.263187231659-0.183792507059-0.4206052139680.6691003848720.7664491562830.3264100893450.4509651650960.1111202137350.02191693129790.671977794027-0.07816040361830.548470225563-3.01080772452-30.832894185-17.4384374666
34.1606762681-0.89152336127-0.5405706005722.249274366990.3417952609192.144716728540.006924453972860.2517643175940.006644791235370.16912589659-0.046929362689-0.7732728422070.2346039666221.250412373160.02418773053460.3761217704240.0106383452865-0.04994173377811.051897960480.1042439268980.6156981234047.1976269337-16.8497428402-18.9443173946
46.73198131253-0.2153995040630.4641944445882.45596124143-0.2420206319773.494945914310.01867251991670.704903007819-0.328471383994-0.2554637108660.03692994473920.3873542401940.224537351541-0.441393079687-0.07718504846110.352326455819-0.0398111860523-0.04489951277920.508298489961-0.000686525271110.427809280779-31.604093523-21.4690975516-18.0315104976
52.913451892612.137320593650.1056853750814.53143912758-0.1838880096644.681092013980.56252795105-0.0148209141070.5955051692-0.1343220914840.129812385702-0.556001483878-1.12357520251-0.459610822876-0.7667919435630.6987639050390.09827577464360.1120073546190.654061390894-0.0551583732290.809626706294-33.36695740892.33712662183-9.40828905683
64.52494389808-0.15941902007-0.5357614204721.938555279030.0855218515073.198054599750.1311319315370.2378092628950.7158758896540.06152438387340.1330752713080.637438296737-0.602984364107-0.963365062484-0.2346137527430.3680359535940.1129721506640.038824616730.6364040315420.1047433123360.616285503502-39.2510824323-5.52224785136-10.0471599309
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 146 )AA2 - 1461 - 143
22chain 'A' and (resid 147 through 224 )AA147 - 224144 - 221
33chain 'A' and (resid 225 through 315 )AA225 - 315222 - 312
44chain 'B' and (resid 2 through 147 )BE2 - 1471 - 141
55chain 'B' and (resid 148 through 188 )BE148 - 188142 - 177
66chain 'B' and (resid 189 through 315 )BE189 - 315178 - 293

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