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- PDB-3hul: Structure of putative homoserine kinase thrB from Listeria monocy... -

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Basic information

Entry
Database: PDB / ID: 3hul
TitleStructure of putative homoserine kinase thrB from Listeria monocytogenes
ComponentsHomoserine kinase
KeywordsTRANSFERASE / structural genomics / putative homoserine kinase / thrB / Amino-acid biosynthesis / ATP-binding / Cytoplasm / Kinase / Nucleotide-binding / Threonine biosynthesis / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative homoserine kinase thrB from Listeria monocytogenes
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionJun 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 kinase
B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4395
Polymers64,1512
Non-polymers2883
Water1,00956
1
A: Homoserine kinase
B: Homoserine kinase
hetero molecules

A: Homoserine kinase
B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,87810
Polymers128,3024
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area12120 Å2
ΔGint-167 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.488, 61.912, 96.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Homoserine kinase / HSK / HK


Mass: 32075.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: thrB, lmo2545 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y4A6, homoserine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, 0.2M Lithium Sulfate, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 31567 / Num. obs: 31567 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.113 / Rsym value: 0.078 / Χ2: 1.097 / Net I/σ(I): 21.931
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.289.80.65731120.871100
2.28-2.3710.40.51530900.904100
2.37-2.4810.60.38531080.945100
2.48-2.6110.60.32931190.96100
2.61-2.7710.60.24431140.982100
2.77-2.9910.50.17131461.027100
2.99-3.2910.50.12431481.138100
3.29-3.7610.40.09631551.182100
3.76-4.74100.06732151.255100
4.74-50100.06433601.67899.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→43.44 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.786 / SU B: 6.343 / SU ML: 0.165 / SU R Cruickshank DPI: 0.281 / SU Rfree: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1553 4.9 %RANDOM
Rwork0.226 ---
obs0.228 31526 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.03 Å2 / Biso mean: 37.071 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.19→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 15 56 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224168
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9765688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6835540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38725.089169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08115652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8761520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213108
X-RAY DIFFRACTIONr_mcbond_it0.8091.52719
X-RAY DIFFRACTIONr_mcangle_it1.52624355
X-RAY DIFFRACTIONr_scbond_it2.13131449
X-RAY DIFFRACTIONr_scangle_it3.4234.51332
LS refinement shellResolution: 2.189→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 113 -
Rwork0.259 2047 -
all-2160 -
obs--93.22 %

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