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- PDB-5x9d: Crystal structure of homoserine dehydrogenase in complex with L-c... -

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Basic information

Entry
Database: PDB / ID: 5x9d
TitleCrystal structure of homoserine dehydrogenase in complex with L-cysteine and NAD
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / Complex / Inhibitor
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
Chem-80F / L(+)-TARTARIC ACID / homoserine dehydrogenase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGoto, M. / Ogata, K. / Kaneko, R. / Yoshimune, K.
CitationJournal: Sci Rep / Year: 2018
Title: Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex
Authors: Ogata, K. / Yajima, Y. / Nakamura, S. / Kaneko, R. / Goto, M. / Ohshima, T. / Yoshimune, K.
History
DepositionMar 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3463
Polymers33,4111
Non-polymers9352
Water2,270126
1
A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6926
Polymers66,8232
Non-polymers1,8694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area3050 Å2
ΔGint-18 kcal/mol
Surface area22200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.171, 106.171, 56.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

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Components

#1: Protein Homoserine dehydrogenase /


Mass: 33411.496 Da / Num. of mol.: 1
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, ST1519, STK_15190 / Plasmid: pET101 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F9VNG5, homoserine dehydrogenase
#2: Chemical ChemComp-80F / (2R)-3-[[(4S)-3-aminocarbonyl-1-[(2R,3R,4S,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4H-pyridin-4-yl]sulfanyl]-2-azanyl-propanoic acid


Mass: 784.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N8O16P2S
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, di-ammonium tartrate

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→75.074 Å / Num. all: 18629 / Num. obs: 18629 / % possible obs: 100 % / Redundancy: 7.5 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.087 / Rsym value: 0.08 / Net I/av σ(I): 8.9 / Net I/σ(I): 18.4 / Num. measured all: 139123
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.217.50.9320.82038727090.36310.9322.3100
2.21-2.357.50.5611.41923925520.2190.6030.5613.7100
2.35-2.517.50.3812.11828624260.1490.4090.3815.3100
2.51-2.717.50.2473.21666322090.0970.2660.2478.1100
2.71-2.977.50.1375.71559320710.0540.1470.13713.7100
2.97-3.327.50.0799.81411618860.0310.0840.07922.9100
3.32-3.837.40.04416.21224516530.0170.0480.04438.2100
3.83-4.77.30.03320.21032514160.0130.0360.03350.4100
4.7-6.647.20.03120.3788910950.0130.0340.03149100
6.64-36.4497.20.02126.643806120.0090.0230.02161.399.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YDR

4ydr


Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2096 / WRfactor Rwork: 0.1678 / FOM work R set: 0.8101 / SU B: 5.914 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2281 / SU Rfree: 0.1912 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 931 5 %RANDOM
Rwork0.1896 ---
obs0.1919 17691 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.71 Å2 / Biso mean: 38.488 Å2 / Biso min: 18.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å2-0 Å2-0 Å2
2--0.57 Å2-0 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 2.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 61 126 2473
Biso mean--30.9 43.01 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022386
X-RAY DIFFRACTIONr_angle_refined_deg1.4522.0133238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07725.05395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57915397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9941512
X-RAY DIFFRACTIONr_chiral_restr0.1470.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211746
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 71 -
Rwork0.299 1301 -
all-1372 -
obs--100 %

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