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- PDB-3d5t: Crystal structure of malate dehydrogenase from Burkholderia pseud... -

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Basic information

Entry
Database: PDB / ID: 3d5t
TitleCrystal structure of malate dehydrogenase from Burkholderia pseudomallei
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / NIAID / deCODE biostructures / Malate Dehydrogenase / NAD / Tricarboxylic acid cycle / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 2 / 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 ...Malate dehydrogenase, type 2 / 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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Malate Dehydrogenase from Burkholderia pseudomallei.
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4656
Polymers141,4184
Non-polymers472
Water7,692427
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7564
Polymers70,7092
Non-polymers472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-17.8 kcal/mol
Surface area24090 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)70,7092
Polymers70,7092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-17.1 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.387, 79.608, 288.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Malate dehydrogenase


Mass: 35354.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His tag cleaved off / Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: mdh, BURPS1710b_A0795 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3JKE9, malate dehydrogenase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.71
Details: 0.1 M Tris-HCl pH 7.71, 32% PEG 4000, 0.2 M MgCl2, 34.5 mg/mL Protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2008 / Details: Adjustable focus K-B pair Si plus Pt, Rh coatings
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 42919 / % possible obs: 89.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.109 / Χ2: 1.258 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.593.60.4372.537921.09980.1
2.59-2.693.70.38739731.1285.1
2.69-2.823.80.31441460.99987.3
2.82-2.963.80.24342080.99589.8
2.96-3.153.80.18342321.02389.7
3.15-3.393.70.13242991.11490.7
3.39-3.733.60.10143141.35590.4
3.73-4.273.60.08144161.54992.2
4.27-5.383.60.06645921.52394.5
5.38-503.70.04649471.70696.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y7T

1y7t


Resolution: 2.51→47.62 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.246 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.898 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2181 5.1 %RANDOM
Rwork0.178 ---
obs0.181 42841 89.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.238 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2--2.18 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.51→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9579 0 2 427 10008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229743
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.97213244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76151278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07324.527391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.176151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7091561
X-RAY DIFFRACTIONr_chiral_restr0.1050.21548
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217325
X-RAY DIFFRACTIONr_mcbond_it0.7861.56384
X-RAY DIFFRACTIONr_mcangle_it1.498210182
X-RAY DIFFRACTIONr_scbond_it2.51733359
X-RAY DIFFRACTIONr_scangle_it4.0934.53062
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 141 -
Rwork0.206 2430 -
all-2571 -
obs--73.04 %

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