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- PDB-5avo: Crystal structure of the reduced form of homoserine dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5avo
TitleCrystal structure of the reduced form of homoserine dehydrogenase from Sulfolobus tokodaii.
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / Reduced form
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding / metal ion binding
Similarity search - Function
Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, conserved site / Homoserine dehydrogenase signature. / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
homoserine dehydrogenase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoto, M. / Yoshimune, K. / Kaneko, R.
CitationJournal: Biochem Biophys Rep / Year: 2015
Title: Structural insight into activation of homoserine dehydrogenase from the archaeonSulfolobus tokodaiivia reduction.
Authors: Tomonaga, Y. / Kaneko, R. / Goto, M. / Ohshima, T. / Yoshimune, K.
History
DepositionJun 25, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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: Homoserine dehydrogenase
B: Homoserine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)66,8232
Polymers66,8232
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-14 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.401, 79.472, 65.899
Angle α, β, γ (deg.)90.000, 107.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Homoserine dehydrogenase


Mass: 33411.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7) (archaea)
Strain: DSM 16993 / JCM 10545 / NBRC 100140 / 7 / Gene: hom, STK_15190 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F9VNG5, homoserine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: PEG 2000, magnesium chloride, PEG 400, 1,4-butanediol

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 47593 / % possible obs: 90.6 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.047 / Rrim(I) all: 0.078 / Χ2: 2.668 / Net I/av σ(I): 28.668 / Net I/σ(I): 13.7 / Num. measured all: 119944
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.832.40.26124710.9110.1960.3281.21294.8
1.83-1.862.50.28424720.9070.2060.3531.60195.3
1.86-1.92.60.21125230.9420.1480.2591.44795.4
1.9-1.942.60.17524990.950.1250.2161.51795.6
1.94-1.982.70.15324810.960.110.191.68994.6
1.98-2.032.60.13924540.9610.10.1721.98494.4
2.03-2.082.60.12324770.9680.0890.1532.29994.7
2.08-2.132.60.11124750.9750.080.1382.27293.9
2.13-2.22.60.10324120.9760.0750.1282.62292.2
2.2-2.272.50.09624320.9790.0710.122.6592.8
2.27-2.352.50.08923650.9830.0670.1122.94391
2.35-2.442.30.08224290.980.0650.1053.02691.8
2.44-2.552.40.0823650.9820.060.1013.15290.8
2.55-2.692.40.07623720.9840.0570.0953.62590.6
2.69-2.862.70.0724250.9870.050.0863.71991.4
2.86-3.082.50.06322920.9870.0460.0783.60687.3
3.08-3.392.50.05723230.990.0420.0713.63588
3.39-3.882.50.05222320.990.0380.0653.80384.4
3.88-4.882.30.04920510.9910.0380.0634.08677.4
4.88-502.50.04820430.9930.0350.063.85175.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefmac_5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDR

4ydr


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / Matrix type: sparse / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.215 / SU B: 3.187 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2426 5.1 %RANDOM
Rwork0.2111 45154 --
obs0.2129 45154 90.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.08 Å2 / Biso mean: 31.185 Å2 / Biso min: 18.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20.84 Å2
2---0.72 Å20 Å2
3----1.13 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 0 162 4662
Biso mean---36.59 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194570
X-RAY DIFFRACTIONr_bond_other_d0.0010.024515
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.9876198
X-RAY DIFFRACTIONr_angle_other_deg0.738310352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72124.886176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49415777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4521522
X-RAY DIFFRACTIONr_chiral_restr0.0680.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_mcbond_it1.6083.0272391
X-RAY DIFFRACTIONr_mcbond_other1.6073.0272390
X-RAY DIFFRACTIONr_mcangle_it2.4734.5292980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.797-1.8440.3011960.2353345389890.8410.206
1.844-1.8940.2961690.2383417374895.6780.208
1.894-1.9490.2551890.2283321368695.2250.204
1.949-2.0090.2631770.2093170354494.4410.191
2.009-2.0750.2861490.2243143347494.7610.208
2.075-2.1470.2731660.2032979335993.6290.19
2.147-2.2280.2271430.2012855323992.5590.189
2.228-2.3190.2411560.2172698309892.1240.206
2.319-2.4220.2781440.2192582298591.3230.212
2.422-2.540.2831390.2272485287991.1430.221
2.54-2.6770.2321290.2132306269390.420.211
2.677-2.8390.2651270.222236260090.8850.22
2.839-3.0340.2171000.2152060242189.2190.225
3.034-3.2760.2451060.2081841225986.1890.221
3.276-3.5870.233810.2111717208486.2760.223
3.587-4.0080.228790.1941475188282.5720.21
4.008-4.6230.229580.1881233167077.3050.209
4.623-5.650.215650.1931046142278.1290.222
5.65-7.940.281350.226852111279.7660.264
7.94-500.201180.23139364563.7210.283

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