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- PDB-6a2e: Apo structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alph... -

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Basic information

Entry
Database: PDB / ID: 6a2e
TitleApo structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase
ComponentsKdo hydroxylase, KdoO
KeywordsBIOSYNTHETIC PROTEIN / Fe(II)/O2/alphaketoglutarate dependent dioxygenase / KDO2-lipid A dioxygenase / deoxysugar dioxygenase / LPS biosynthesis
Function / homologyKdo hydroxylase / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase / metal ion binding / ACETATE ION / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
Function and homology information
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.939 Å
AuthorsChung, H.S. / Pemble, C.W. / Joo, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Biochemical and Structural Insights into an Fe(II)/ alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO).
Authors: Joo, S.H. / Pemble, C.W. / Yang, E.G. / Raetz, C.R.H. / Chung, H.S.
History
DepositionJun 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 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

Downloads & links

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Assembly

Deposited unit
A: Kdo hydroxylase, KdoO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7076
Polymers36,2391
Non-polymers4675
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.896, 59.541, 116.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Kdo hydroxylase, KdoO / 3-Deoxy-D-manno-oct-2-ulosonic acid hydroxylase


Mass: 36239.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (isolate V4) (bacteria)
Strain: V4 / Gene: Minf_1012 / Production host: Escherichia coli (E. coli) / References: UniProt: B3DUR4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium acetate, 200mM Lithium sulfate, 50% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.939→50 Å / Num. obs: 24341 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 18.21 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.735 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.94-1.975.20.2815.1610381.13987.1
1.97-2.016.20.26812021.02399.7
2.01-2.057.10.23712021.054100
2.05-2.096.70.27512191.947100
2.09-2.147.30.19512021.157100
2.14-2.187.30.18111971.205100
2.18-2.247.10.16811931.22999.7
2.24-2.36.60.21712162.58499.9
2.3-2.377.30.14111971.383100
2.37-2.447.30.13712151.384100
2.44-2.537.30.12812111.514100
2.53-2.637.30.11612051.70999.9
2.63-2.757.20.11712281.83799.9
2.75-2.97.30.09812351.7100
2.9-3.087.30.08812231.779100
3.08-3.327.20.08112332.007100
3.32-3.6570.08512402.776100
3.65-4.186.90.08912543.63299.9
4.18-5.267.10.06312642.183100
5.26-506.60.04113671.19199.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.939→41.605 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.19
RfactorNum. reflection% reflection
Rfree0.2052 1197 5.03 %
Rwork0.1566 --
obs0.159 23780 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.08 Å2 / Biso mean: 23.8371 Å2 / Biso min: 8.35 Å2
Refinement stepCycle: final / Resolution: 1.939→41.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 27 252 2665
Biso mean--48.57 33.04 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062489
X-RAY DIFFRACTIONf_angle_d0.7673367
X-RAY DIFFRACTIONf_chiral_restr0.051363
X-RAY DIFFRACTIONf_plane_restr0.006432
X-RAY DIFFRACTIONf_dihedral_angle_d15.2431500
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9394-2.01710.22871240.15732291241591
2.0171-2.10890.21571290.1552413254295
2.1089-2.22010.22381310.14612462259397
2.2201-2.35910.24221290.15732449257897
2.3591-2.54130.19081340.15572526266099
2.5413-2.7970.23551350.1652541267699
2.797-3.20160.18511340.167825662700100
3.2016-4.03310.19761370.148225962733100
4.0331-41.61460.19321440.15727392883100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3208-0.00970.05620.65850.02120.411-0.010.0450.0826-0.103-0.04260.0245-0.0375-0.0148-0.00010.10030.0144-0.00110.11650.0020.10641.73393.40386.3404
20.22520.16180.0380.4585-0.19440.36010.0454-0.01320.014-0.0546-0.02230.04220.0616-0.05070.00190.10280.0046-0.00640.09990.0030.0944-3.0087-11.392317.2609
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 133 )A11 - 133
2X-RAY DIFFRACTION2chain 'A' and (resid 134 through 307 )A134 - 307

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