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- PDB-2x0j: 2.8 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGL... -

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Basic information

Entry
Database: PDB / ID: 2x0j
Title2.8 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH ETHENO-NAD
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HYPERTHERMOPHILIC / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


(S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 3 / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...Malate dehydrogenase, type 3 / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ETHENO-NAD / Malate dehydrogenase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.786 Å
AuthorsIrimia, A. / Madern, D. / Zaccai, G. / Vellieux, F.M. / Karshikoff, A. / Tibbelin, G. / Ladenstein, R. / Lien, T. / Birkeland, N.K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The 2.9A Resolution Crystal Structure of Malate Dehydrogenase from Archaeoglobus Fulgidus: Mechanisms of Oligomerisation and Thermal Stabilisation.
Authors: Irimia, A. / Vellieux, F.M.D. / Madern, D. / Zaccai, G. / Karshikoff, A. / Tibbelin, G. / Ladenstein, R. / Lien, T. / Birkeland, N.K.
#1: Journal: Biochemistry / Year: 2001
Title: Differences in the Oligomeric States of the Ldh-Like L-Maldh from the Hyperthermophilic Archaea Methanococcus Jannaschii and Archaeoglobus Fulgidus.
Authors: Madern, D. / Ebel, C. / Dale, H.A. / Lien, T. / Steen, I.H. / Birkeland, N.-K. / Zaccai, G.
#2: Journal: Arch.Microbiol. / Year: 1997
Title: Properties and Primary Structure of a Thermostable L-Malate Dehydrogenase from Archaeoglobus Fulgidus
Authors: Langelandsvik, A.S. / Steen, I.H. / Birkeland, N.K. / Lien, T.
History
DepositionDec 14, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionDec 22, 2009ID: 1OJU
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6973
Polymers31,9141
Non-polymers7842
Water54030
1
A: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3956
Polymers63,8282
Non-polymers1,5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6630 Å2
ΔGint-63.13 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.990, 112.990, 70.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MALATE DEHYDROGENASE


Mass: 31913.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea)
Plasmid: PSJS1240 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ONE SHOT
References: UniProt: O08349, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#2: Chemical ChemComp-ENA / ETHENO-NAD


Type: RNA linking / Mass: 687.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N7O14P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 62.22 % / Description: NONE
Crystal growpH: 4
Details: INITIAL PROTEIN DROPLET: 22 MG/ML PROTEIN, 10 MM ETHENO-NAD RESERVOIR: 1.6 % (W/V) POLYETHYLENE GLYCOL 8000, 0.8 M LISO4 DROPLET: EQUAL VOLUMES OF INITIAL PROTEIN DROPLET AND RESERVOIR, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.79→35.8 Å / Num. obs: 10861 / % possible obs: 90.9 % / Observed criterion σ(I): 0.5 / Redundancy: 15.5 % / Biso Wilson estimate: 67.74 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 43.5
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 12.7 / % possible all: 71

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
BIOMOLdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.786→35.731 Å / SU ML: 0.34 / σ(F): 2.21 / Phase error: 22.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 585 5.4 %
Rwork0.164 --
obs0.167 10819 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.512 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso mean: 73.59 Å2
Baniso -1Baniso -2Baniso -3
1--12.0764 Å2-0 Å20 Å2
2---12.0764 Å2-0 Å2
3---24.1527 Å2
Refinement stepCycle: LAST / Resolution: 2.786→35.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 51 30 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092322
X-RAY DIFFRACTIONf_angle_d1.2493141
X-RAY DIFFRACTIONf_dihedral_angle_d25.57906
X-RAY DIFFRACTIONf_chiral_restr0.092359
X-RAY DIFFRACTIONf_plane_restr0.006399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7861-3.06630.27471020.23812157X-RAY DIFFRACTION78
3.0663-3.50970.26281440.20172483X-RAY DIFFRACTION90
3.5097-4.42060.22231530.14722727X-RAY DIFFRACTION97
4.4206-35.73350.19071860.14732867X-RAY DIFFRACTION98
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)
11.1918-0.8649-0.79211.52291.0441.8463-0.2645-0.46670.27410.10560.1793-0.26170.2465-0.199-0.00060.30030.001-0.00520.4717-0.08450.300530.300231.646912.093
21.1625-0.5037-1.03331.14870.53580.5908-0.0736-0.26680.25680.04070.0650.23830.11120.0020.02080.3271-0.03-0.01480.5456-0.1160.346315.154840.71612.6724
31.1917-0.42680.53120.54840.11611.28880.1052-0.00630.3769-0.609-0.28570.499-0.41670.11180.2680.6020.06380.05450.38610.03690.564520.859252.2108-8.9829
40.4541-0.86020.51216.7769-1.35232.24050.12280.0398-0.0916-0.1205-0.17161.3556-0.0697-0.4783-0.10090.26720.0299-0.18250.4717-0.06250.450614.782941.6347-11.4245
50.8912-0.32070.19191.2348-1.04560.687-0.0024-0.17390.5566-0.10080.0815-0.05880.05030.1163-0.01280.2025-0.0242-0.0060.3255-0.20960.393122.455749.56887.4221
61.1186-1.12960.1331.1232-0.01781.7965-0.1633-0.22360.3578-0.0006-0.02280.4385-0.3277-0.53730.02940.40460.05850.01910.4635-0.20070.82737.921553.39825.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:103)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 105:172)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 173:219)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 220:244)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 245:297)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 298:331)

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