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- PDB-2x0i: 2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGL... -

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Basic information

Entry
Database: PDB / ID: 2x0i
Title2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NADH
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsIrimia, A. / Madern, D. / Zaccai, G. / Vellieux, F.M.D. / 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: 1OJS
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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)32,6984
Polymers31,9141
Non-polymers7843
Water70339
1
A: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3978
Polymers63,8282
Non-polymers1,5696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6970 Å2
ΔGint-100.41 kcal/mol
Surface area22140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.964, 112.964, 71.294
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 62.93 % / Description: NONE
Crystal growpH: 4
Details: INITIAL PROTEIN DROPLET: 16 MG/ML PROTEIN, 10 MM NADH, 20 M RESERVOIR: 1.6 M AMMONIUM SULPHATE, 20% (V/V) GLYCEROL, 80 M DROPLET: EQUAL VOLUMES OF INITIAL PROTEIN DROPLET AND RESERVOIR WERE MIXED., pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933
DetectorType: ADSC CCD / 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: 2.91→59.76 Å / Num. obs: 8949 / % possible obs: 83.6 % / Observed criterion σ(I): 0.5 / Redundancy: 8.7 % / Biso Wilson estimate: 62.26 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.9
Reflection shellResolution: 2.91→3.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 9.7 / % possible all: 45.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
BIOMOLdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HLP

2hlp


Resolution: 2.91→56.48 Å / SU ML: 0.32 / σ(F): 2.17 / Phase error: 20.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 492 5.5 %
Rwork0.1519 --
obs0.1557 8932 84.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.248 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 62.89 Å2
Baniso -1Baniso -2Baniso -3
1--10.0474 Å20 Å20 Å2
2---10.0474 Å20 Å2
3---20.0947 Å2
Refinement stepCycle: LAST / Resolution: 2.91→56.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 50 39 2326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082319
X-RAY DIFFRACTIONf_angle_d1.4613136
X-RAY DIFFRACTIONf_dihedral_angle_d20.859906
X-RAY DIFFRACTIONf_chiral_restr0.124360
X-RAY DIFFRACTIONf_plane_restr0.006399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9086-3.20130.269770.19711653X-RAY DIFFRACTION67
3.2013-3.66440.22031350.16572125X-RAY DIFFRACTION87
3.6644-4.61650.211160.12842291X-RAY DIFFRACTION91
4.6165-56.49260.20711640.14492371X-RAY DIFFRACTION91
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)
11.0697-0.7768-1.01481.4330.9670.9962-0.2138-0.36140.12480.00710.1517-0.14280.14740.00440.00960.24920.0201-0.01170.3452-0.03540.210330.292931.870612.1162
20.9688-0.5818-0.34470.99870.19980.473-0.1377-0.2786-0.0526-0.0766-0.06930.17150.01120.01340.06920.245-0.0107-0.00090.3397-0.07480.252715.051140.923112.5001
31.1561-0.33520.52740.7646-0.38830.83420.0990.04130.197-0.09-0.338-0.00250.0010.04920.11520.3970.06660.01360.34820.01550.355720.885752.1884-9.3313
40.6085-1.21830.40274.5118-1.33570.9223-0.2450.0665-0.197-0.26950.24361.0068-0.0731-0.148-0.25680.33080.0811-0.22510.4246-0.09080.686814.750441.6763-11.9056
50.5430.0881-0.08820.4174-0.00490.61420.0219-0.12310.2412-0.14330.12710.0186-0.00550.0822-0.12050.2582-0.01010.01250.2514-0.1160.327522.412649.75867.2185
60.5683-0.53250.02050.8092-0.331.2036-0.0753-0.09610.02990.03950.14850.2202-0.3902-0.2652-0.08070.38260.03760.01440.3834-0.13320.69897.809553.54075.112
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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