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- PDB-2bgm: X-Ray structure of ternary-Secoisolariciresinol Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2bgm
TitleX-Ray structure of ternary-Secoisolariciresinol Dehydrogenase
ComponentsRHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
KeywordsXIDOREDUCTASE / OXIDOREDUCTASE / DEHYDROGENASE
Function / homology
Function and homology information


secoisolariciresinol dehydrogenase / (-)-secoisolariciresinol dehydrogenase activity / lignan biosynthetic process / protein homotetramerization / nucleotide binding
Similarity search - Function
Xanthoxin dehydrogenase ABA2-like / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MATAIRESINOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Secoisolariciresinol dehydrogenase
Similarity search - Component
Biological speciesPODOPHYLLUM PELTATUM (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYoun, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures of Apo-Form and Binary/Ternary Complexes of Podophyllum Secoisolariciresinol Dehydrogenase, an Enzyme Involved in Formation of Health-Protecting and Plant Defense Lignans
Authors: Youn, B. / Moinuddin, S.G. / Davin, L.B. / Lewis, N.G. / Kang, C.
History
DepositionDec 23, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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

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Assembly

Deposited unit
A: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3073
Polymers29,2851
Non-polymers1,0222
Water2,288127
1
A: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
hetero molecules

A: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
hetero molecules

A: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
hetero molecules

A: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,22812
Polymers117,1414
Non-polymers4,0878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.350, 118.740, 131.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2029-

HOH

21A-2115-

HOH

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Components

#1: Protein RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE


Mass: 29285.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PODOPHYLLUM PELTATUM (plant) / Plasmid: PTRCHIS2-TOPO TA VECTOR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: Q94KL8
#2: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#3: Chemical ChemComp-MAX / MATAIRESINOL / ARTIGENIN CONGENER / DIBENZYLBUTYROLACTONE LIGNANOLIDE / Matairesinol


Mass: 358.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU STURN 92 / Wavelength: 1.54
DetectorType: RIGAKU CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12187 / % possible obs: 79.1 % / Observed criterion σ(I): 2 / Redundancy: 5.81 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.2 / % possible all: 13.1

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BGK

1bgk


Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.229 -5 %RANDOM
Rwork0.2 ---
obs0.2 11716 79.1 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 70 127 2182
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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