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- PDB-3i0p: Crystal structure of malate dehydrogenase from Entamoeba histolytica -

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Basic information

Entry
Database: PDB / ID: 3i0p
TitleCrystal structure of malate dehydrogenase from Entamoeba histolytica
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / araerobic parasitic protozoan / amoebic dysentery / SSGCID / NIAID / Infectious disease / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich ...Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of malate dehydrogenase from Entamoeba histolytica
Authors: Edwards, T.E. / Abendroth, J. / Staker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)41,2543
Polymers40,4981
Non-polymers7562
Water1,76598
1
A: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5076
Polymers80,9962
Non-polymers1,5114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area10490 Å2
ΔGint-81 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.230, 106.230, 72.114
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
DetailsDimer

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Components

#1: Protein Malate dehydrogenase


Mass: 40498.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): AVA0421 / References: UniProt: C4M213*PLUS
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNP SEQUENCE REFERENCE IS NOT AVAILABLE AT THE TIME OF PROCESSING. THE DEPOSITED SEQUENCE ...THE UNP SEQUENCE REFERENCE IS NOT AVAILABLE AT THE TIME OF PROCESSING. THE DEPOSITED SEQUENCE CORRESPONDS TO THE SEQUENCE OF GB ENTRY XP_649756.2.

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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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ sparse matrix screen condition a2, 20% PEG 3000, 0.1 M Na Citrate pH 5.5, 25% glycerol as cryo-protectant, 30 mg/mL protein, crystal ID 203003a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorDate: May 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→38.78 Å / Num. obs: 14659 / % possible obs: 99.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.144 / Χ2: 1.072 / Net I/σ(I): 13.75
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.18 / Num. unique all: 1371 / Χ2: 1.098 / % possible all: 94.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.73 Å38.78 Å
Translation2.73 Å38.78 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1v9n

1v9n


Resolution: 2.6→38.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.841 / SU B: 9.586 / SU ML: 0.201 / SU R Cruickshank DPI: 0.568 / SU Rfree: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.568 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.232 732 5 %RANDOM
Rwork0.182 ---
obs0.184 14657 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.42 Å2 / Biso mean: 27.582 Å2 / Biso min: 9.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.7 Å20 Å2
2--1.4 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2793 0 50 98 2941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222911
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9863931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88924.331127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30515506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7481516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212185
X-RAY DIFFRACTIONr_mcbond_it0.4271.51791
X-RAY DIFFRACTIONr_mcangle_it0.83222882
X-RAY DIFFRACTIONr_scbond_it1.19331120
X-RAY DIFFRACTIONr_scangle_it2.0794.51049
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 46 -
Rwork0.3 981 -
all-1027 -
obs--93.7 %

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