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- PDB-3nep: 1.55A resolution structure of malate dehydrogenase from Salinibac... -

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Basic information

Entry
Database: PDB / ID: 3nep
Title1.55A resolution structure of malate dehydrogenase from Salinibacter ruber
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Malate dehydrogenase / halophile / molecular adpatation / NAD / tricarboxylic acid cycle
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 3 / 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 3 / 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 speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.551 Å
AuthorsCoquelle, N. / Madern, D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Gradual adaptive changes of a protein facing high salt concentrations.
Authors: Coquelle, N. / Talon, R. / Juers, D.H. / Girard, E. / Kahn, R. / Madern, D.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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
X: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)33,2871
Polymers33,2871
Non-polymers00
Water6,125340
1
X: Malate dehydrogenase

X: Malate dehydrogenase

X: Malate dehydrogenase

X: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)133,1464
Polymers133,1464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area13690 Å2
ΔGint-53 kcal/mol
Surface area41550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.110, 87.720, 100.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11X-1305-

HOH

21X-1306-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 33286.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Salinibacter ruber (bacteria) / Strain: DSM 13855 / References: UniProt: Q2S289, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1M LiCl, 0.1M Citric Acid, 10% PEG 6000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.9797
SYNCHROTRONESRF ID2920.932
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDSep 5, 2007mirror
ADSC QUANTUM 315r2CCDSep 21, 2007mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111) or Si (311)SINGLE WAVELENGTHMx-ray1
2Si (111) or Si (311)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.9321
ReflectionResolution: 1.55→43.9 Å / Num. all: 47819 / Num. obs: 47819 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.36 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.39
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 4 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.23 / Num. unique all: 4131 / % possible all: 93.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.6_288)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUZ

1guz


Resolution: 1.551→33.036 Å / SU ML: 0.16 / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 2258 4.72 %Random
Rwork0.168 ---
obs0.1691 47804 97.65 %-
all-47819 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Solvent model: FLAT BULK SOLVENT MODEL HYDROGENS ADDED IN THE RIDING POSITION DURING REFINEMENT
Bsol: 67.273 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3884 Å2-0 Å20 Å2
2---5.3636 Å2-0 Å2
3---1.9753 Å2
Refinement stepCycle: LAST / Resolution: 1.551→33.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2263 0 0 340 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132408
X-RAY DIFFRACTIONf_angle_d1.3333296
X-RAY DIFFRACTIONf_dihedral_angle_d14.726909
X-RAY DIFFRACTIONf_chiral_restr0.082389
X-RAY DIFFRACTIONf_plane_restr0.007442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.551-1.60640.30352250.25344388X-RAY DIFFRACTION96
1.6064-1.67080.27242320.22794514X-RAY DIFFRACTION98
1.6708-1.74680.26462290.20494495X-RAY DIFFRACTION98
1.7468-1.83890.22682300.19254482X-RAY DIFFRACTION97
1.8389-1.95410.23772160.19534510X-RAY DIFFRACTION97
1.9541-2.10490.20022260.16544528X-RAY DIFFRACTION98
2.1049-2.31670.1772170.15134579X-RAY DIFFRACTION98
2.3167-2.65180.17452250.14414597X-RAY DIFFRACTION98
2.6518-3.34050.16112260.15374657X-RAY DIFFRACTION99
3.3405-33.04380.17382320.16224796X-RAY DIFFRACTION98

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