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- PDB-1bg6: CRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDR... -

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Basic information

Entry
Database: PDB / ID: 1bg6
TitleCRYSTAL STRUCTURE OF THE N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE FROM ARTHROBACTER SP. STRAIN 1C
ComponentsN-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / (D / L) STEREOSPECIFIC OPINE DEHYDROGENASE
Function / homology
Function and homology information


opine dehydrogenase / opine dehydrogenase activity
Similarity search - Function
Opine dehydrogenase / NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Opine dehydrogenase / NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArthrobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsBritton, K.L. / Asano, Y. / Rice, D.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure and active site location of N-(1-D-carboxylethyl)-L-norvaline dehydrogenase.
Authors: Britton, K.L. / Asano, Y. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of Arthrobacter Sp. Strain 1C N-(1-D-Carboxyethyl)-L-Norvaline Dehydrogenase and its Complex with Nad+
Authors: Britton, K.L. / Rogers, H.F. / Asano, Y. / Dairi, T. / Kato, Y. / Stillman, T.J. / Rice, D.W.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)37,9691
Polymers37,9691
Non-polymers00
Water2,036113
1
A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE

A: N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)75,9382
Polymers75,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)104.900, 80.000, 45.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-(1-D-CARBOXYLETHYL)-L-NORVALINE DEHYDROGENASE


Mass: 37969.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter sp. (bacteria) / Strain: 1C / Gene: ODH / Plasmid: PODH1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44297
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.65 Å3/Da / Density % sol: 41 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Mpotassium phosphate1drop
336-37 %satammonium sulfate1reservoir
40.1 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→16 Å / Num. obs: 30854 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 2.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5 / % possible all: 78
Reflection
*PLUS
Num. measured all: 66518
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
all31467 -
obs28922 83 %
Solvent computationBsol: 310 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2592 0 0 113 2705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg1.65
X-RAY DIFFRACTIONt_dihedral_angle_d17.47
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2545 / % reflection Rfree: 8 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.263
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.47
X-RAY DIFFRACTIONt_plane_restr0.016

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