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- PDB-3asu: Crystal structure of serine dehydrogenase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3asu
TitleCrystal structure of serine dehydrogenase from Escherichia coli
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SDR family / Rossmann-fold / short-chain dehydrogenase/reductase / L-allo-threonine dehydrogenase
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsYamazawa, R. / Nakajima, Y. / Yoshimoto, T. / Ito, K.
CitationJournal: J.Biochem. / Year: 2011
Title: Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation.
Authors: Yamazawa, R. / Nakajima, Y. / Mushiake, K. / Yoshimoto, T. / Ito, K.
History
DepositionDec 21, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 1, 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: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)54,5562
Polymers54,5562
Non-polymers00
Water4,414245
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR


Theoretical massNumber of molelcules
Total (without water)109,1124
Polymers109,1124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area13230 Å2
ΔGint-75 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.79, 66.79, 175.9
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 27277.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1-Blue / Gene: EcDH1_2106, YdfG / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: EC: 1.1.1.276
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (ESCHERICHIA COLI XL1-BLUE) DOES NOT CURRENTLY EXIST IN UNIPROT

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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: 2.08 Å3/Da / Density % sol: 40.75 % / Mosaicity: 0.354 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 400, MgCl2, HEPES-Na buffer, pH 7.6, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 36558 / % possible obs: 99.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.073 / Χ2: 1.077 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.93110.34317660.331100
1.93-1.97110.2818090.3581100
1.97-2.01110.25818020.3881100
2.01-2.05110.21417890.4361100
2.05-2.09110.19718180.4331100
2.09-2.14110.16818130.5031100
2.14-2.1911.10.15117770.541100
2.19-2.25110.12418210.6171100
2.25-2.32110.11218230.661100
2.32-2.39110.10818040.6951100
2.39-2.48110.09818390.8131100
2.48-2.58110.0918010.9181100
2.58-2.7110.08418350.9991100
2.7-2.8410.90.07718281.1961100
2.84-3.0210.90.07218431.4721100
3.02-3.2510.80.06718431.752199.9
3.25-3.5810.70.05918412.094199.9
3.58-4.0910.50.05318972.355199.9
4.09-5.1610.10.0518742.549199
5.16-509.10.05419352.731195.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
CNS1.2refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWQ

2nwq


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 2222897 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1823 5 %RANDOM
Rwork0.2 ---
obs-36484 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.2996 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 57.29 Å2 / Biso mean: 26.9565 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.2 Å20 Å2
3----6.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 0 245 3577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 294 5 %
Rwork0.225 5539 -
all-5833 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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