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- PDB-5kka: E. coli malate dehydrogenase with the inhibitor 6DHNAD -

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Basic information

Entry
Database: PDB / ID: 5kka
TitleE. coli malate dehydrogenase with the inhibitor 6DHNAD
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate / dehydrogenase / 6DHNAD / inhibitor / beta- 6-dihydronicotimide adenine dinucleotide
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
Chem-6V0 / Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMeneely, K.M. / Lamb, A.L. / Moran, G.R.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1402475 United States
UWM Research Grown Initiative United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K02 AI093675 United States
National Science Foundation (NSF, United States)CHE-1403293 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Ligand binding phenomena that pertain to the metabolic function of renalase.
Authors: Beaupre, B.A. / Roman, J.V. / Hoag, M.R. / Meneely, K.M. / Silvaggi, N.R. / Lamb, A.L. / Moran, G.R.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0674
Polymers64,7362
Non-polymers1,3312
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-32 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.530, 83.832, 89.275
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Malate dehydrogenase


Mass: 32368.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mdh, b3236, JW3205 / Production host: Escherichia coli (E. coli) / References: UniProt: P61889, malate dehydrogenase
#2: Chemical ChemComp-6V0 / [[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate / 6DHNAD


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, pH 6.0, 21% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2016 / Details: Rh coated flat, toroidal focusing
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→39.4 Å / Num. obs: 58987 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.6 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
XDSdata scaling
PHENIX1.10_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHP

3hhp


Resolution: 1.75→39.4 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.84
RfactorNum. reflection% reflection
Rfree0.1807 2001 3.4 %
Rwork0.1545 --
obs0.1554 58919 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.34 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 88 473 4924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014532
X-RAY DIFFRACTIONf_angle_d1.1036163
X-RAY DIFFRACTIONf_dihedral_angle_d12.3072707
X-RAY DIFFRACTIONf_chiral_restr0.057753
X-RAY DIFFRACTIONf_plane_restr0.007787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7483-1.79210.21751310.19293869X-RAY DIFFRACTION95
1.7921-1.84050.23061500.18073993X-RAY DIFFRACTION99
1.8405-1.89470.22871310.17914032X-RAY DIFFRACTION99
1.8947-1.95580.21091370.16774031X-RAY DIFFRACTION99
1.9558-2.02570.1971460.1634025X-RAY DIFFRACTION99
2.0257-2.10680.17791440.15054063X-RAY DIFFRACTION99
2.1068-2.20270.19271470.14664039X-RAY DIFFRACTION100
2.2027-2.31880.19511450.14194057X-RAY DIFFRACTION99
2.3188-2.46410.18031410.14434077X-RAY DIFFRACTION99
2.4641-2.65430.17371380.14684054X-RAY DIFFRACTION99
2.6543-2.92130.19571410.15674117X-RAY DIFFRACTION100
2.9213-3.34390.1871500.15864123X-RAY DIFFRACTION99
3.3439-4.21220.14621480.14344117X-RAY DIFFRACTION99
4.2122-39.41020.15361520.1554321X-RAY DIFFRACTION99

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