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- PDB-7f4b: The crystal structure of the immature apo-enzyme of homoserine de... -

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Basic information

Entry
Database: PDB / ID: 7f4b
TitleThe crystal structure of the immature apo-enzyme of homoserine dehydrogenase from the hyperthermophilic archaeon Sulfurisphaera tokodaii.
Componentshomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / heat-induced activation
Biological speciesSulfurisphaera tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKurihara, E. / Kubota, T. / Watanabe, K. / Ogata, K. / Kaneko, R. / Oshima, T. / Yoshimune, K. / Goto, M.
CitationJournal: Commun Biol / Year: 2022
Title: Conformational changes in the catalytic region are responsible for heat-induced activation of hyperthermophilic homoserine dehydrogenase.
Authors: Kubota, T. / Kurihara, E. / Watanabe, K. / Ogata, K. / Kaneko, R. / Goto, M. / Ohshima, T. / Yoshimune, K.
History
DepositionJun 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: homoserine dehydrogenase
B: homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8724
Polymers66,8232
Non-polymers492
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-20 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.098, 78.305, 65.551
Angle α, β, γ (deg.)90.000, 106.170, 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.) Sulfurisphaera tokodaii (archaea) / Plasmid: pET101 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: homoserine dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG2000, magnesium chloride, PEG400, Tris-HCl, DMSO

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→62.958 Å / Num. obs: 34762 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Rsym value: 0.068 / Net I/av σ(I): 8.3 / Net I/σ(I): 10.9 / Num. measured all: 128270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.163.80.5791.41900050430.3450.6760.5792.299.9
2.16-2.293.80.4051.91822847960.2390.4710.4053.299.9
2.29-2.453.60.2892.71638045200.1760.340.2894.299.8
2.45-2.653.80.2113.71571741870.1260.2470.2115.699.8
2.65-2.93.80.1335.81465338630.0790.1550.1338.599.7
2.9-3.243.60.0878.61241434730.0540.1030.08712.299.3
3.24-3.743.70.05412.71137230970.0320.0630.05420.299.6
3.74-4.583.50.04114.7905725970.0250.0480.04127.398.8
4.58-6.483.60.03416.9739320420.020.0390.03429.999.6
6.48-44.9193.50.02620.4405611440.0160.0310.02634.399.2

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AVO

5avo


Resolution: 2.05→48.59 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.069 / SU ML: 0.211 / SU R Cruickshank DPI: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2813 1682 4.8 %RANDOM
Rwork0.2314 ---
obs0.2339 33061 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.41 Å2 / Biso mean: 44.944 Å2 / Biso min: 20.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.05 Å2
2---0.12 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.05→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4457 0 2 164 4623
Biso mean--45.93 47.07 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194527
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9866143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78325.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22615763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4791520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213347
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 131 -
Rwork0.357 2426 -
all-2557 -
obs--100 %

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