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- PDB-3hhp: Malate dehydrogenase open conformation -

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Basic information

Entry
Database: PDB / ID: 3hhp
TitleMalate dehydrogenase open conformation
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / MDH / citric acid cycle / TCA cycle / NAD / Tricarboxylic acid cycle
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity ...malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity / protein homodimerization activity / membrane / cytosol / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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
Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsZaitseva, J. / Meneely, K.M. / Lamb, A.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of Escherichia coli malate dehydrogenase at 1.45 A resolution.
Authors: Zaitseva, J. / Meneely, K.M. / Lamb, A.L.
History
DepositionMay 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)129,4734
Polymers129,4734
Non-polymers00
Water9,458525
1
A: Malate dehydrogenase
B: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)64,7362
Polymers64,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area23760 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)64,7362
Polymers64,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-26 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.026, 51.972, 168.980
Angle α, β, γ (deg.)90.000, 102.230, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Malate dehydrogenase


Mass: 32368.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mdh, b3236, JW3205 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61889, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM ADA, 0.2 M sodium acetate, 30% PEG MME 5000, 5% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→60.971 Å / Num. obs: 215865 / % possible obs: 98.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.45→1.49 Å / Mean I/σ(I) obs: 1.5 / Num. unique all: 216241 / Rsym value: 0.417 / % possible all: 94.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→60.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.253 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 21468 9.9 %RANDOM
Rwork0.186 ---
obs0.188 215852 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.43 Å2 / Biso mean: 17.652 Å2 / Biso min: 3.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→60.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 0 525 9989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0229654
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.98913198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2951379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44126.336363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.961151711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4541534
X-RAY DIFFRACTIONr_chiral_restr0.1440.21594
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217225
X-RAY DIFFRACTIONr_mcbond_it1.3151.56391
X-RAY DIFFRACTIONr_mcangle_it2.077210333
X-RAY DIFFRACTIONr_scbond_it3.43333263
X-RAY DIFFRACTIONr_scangle_it5.6134.52811
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 1512 -
Rwork0.339 13842 -
all-15354 -
obs--94.4 %

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