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- PDB-1xdw: NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidamin... -

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Basic information

Entry
Database: PDB / ID: 1xdw
TitleNAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase from Acidaminococcus fermentans
ComponentsNAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase
KeywordsOXIDOREDUCTASE / structural variant of the bab Rossmann fold
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesAcidaminococcus fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsMartins, B.M. / Macedo-Ribeiro, S. / Bresser, J. / Buckel, W. / Messerschmidt, A.
CitationJournal: Febs J. / Year: 2005
Title: Structural basis for stereo-specific catalysis in NAD(+)-dependent (R)-2-hydroxyglutarate dehydrogenase from Acidaminococcus fermentans.
Authors: Martins, B.M. / Macedo-Ribeiro, S. / Bresser, J. / Buckel, W. / Messerschmidt, A.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)36,6311
Polymers36,6311
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.490, 67.490, 312.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein NAD+-dependent (R)-2-Hydroxyglutarate Dehydrogenase


Mass: 36631.152 Da / Num. of mol.: 1 / Fragment: HGDH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Gene: hgh / Production host: Escherichia coli (E. coli)
References: Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15-18 % PEG MME 2000 or PEG 2000, and 0.2 M sodium or lithium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.2545, 1.2555, 1.0500
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.25451
21.25551
31.051
ReflectionResolution: 1.98→20 Å / Num. all: 30959 / Num. obs: 28589 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17.2 % / Biso Wilson estimate: 20.99 Å2 / Rsym value: 0.053 / Net I/σ(I): 28.17
Reflection shellResolution: 1.98→2.031 Å / Mean I/σ(I) obs: 6.84 / Num. unique all: 1728 / Rsym value: 0.316 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.98→19.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.171 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22532 1492 5 %RANDOM
Rwork0.17726 ---
obs0.17966 28589 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.999 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.55 Å20 Å2
2--1.09 Å20 Å2
3----1.64 Å2
Refinement stepCycle: LAST / Resolution: 1.98→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 0 403 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222543
X-RAY DIFFRACTIONr_bond_other_d0.0020.022329
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9643444
X-RAY DIFFRACTIONr_angle_other_deg0.87935400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9435330
X-RAY DIFFRACTIONr_chiral_restr0.1210.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022862
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02496
X-RAY DIFFRACTIONr_nbd_refined0.2410.2546
X-RAY DIFFRACTIONr_nbd_other0.2570.22744
X-RAY DIFFRACTIONr_nbtor_other0.0860.21458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.232
X-RAY DIFFRACTIONr_mcbond_it1.1441.51635
X-RAY DIFFRACTIONr_mcangle_it1.85122622
X-RAY DIFFRACTIONr_scbond_it3.0423908
X-RAY DIFFRACTIONr_scangle_it4.7124.5822
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.357 95
Rwork0.301 1728

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