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- PDB-5y9x: Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) ... -

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Basic information

Entry
Database: PDB / ID: 5y9x
TitleCrystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and coblat(II)
ComponentsUncharacterized protein 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 / ACETATE ION / 2-OXOGLUTARIC ACID / : / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
Function and homology information
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.39 Å
AuthorsChung, H.S. / Pemble, C.W. / Joo, S.H. / Raetz, C.R.
CitationJournal: To Be Published
Title: Biochemical and structural insights of Fe(II)/alpha-ketoglutarate/O2-dependent dioxygenase, KdoO from Methylacidiphilum infernorum V4
Authors: Chung, H.S. / Pemble IV, C.W. / Joo, S.H.
History
DepositionAug 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein KdoO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,06220
Polymers36,2391
Non-polymers1,82319
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.038, 59.263, 116.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein 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: isolate V4 / Gene: Minf_1012 / Production host: Escherichia coli (E. coli) / References: UniProt: B3DUR4

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Non-polymers , 8 types, 339 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 43.79 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium acetate (pH 4.5), 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: Jul 31, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 61166 / % possible obs: 93.9 % / Redundancy: 7 % / Biso Wilson estimate: 10.01 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.081 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.39-1.414.30.43326220.869181.5
1.41-1.444.90.42226570.921182.9
1.44-1.475.40.39827260.944185.8
1.47-1.560.36727660.976185.9
1.5-1.536.50.31828830.955189.4
1.53-1.576.80.30229310.977191
1.57-1.66.90.26529860.964193.1
1.6-1.657.10.23630530.97194
1.65-1.77.10.20730580.99194.9
1.7-1.757.20.17530960.991196.1
1.75-1.817.20.14231230.954196.4
1.81-1.897.20.12231370.965197.3
1.89-1.977.30.09531790.954197.7
1.97-2.087.50.08131831.032197.6
2.08-2.217.50.07132071.086197.8
2.21-2.387.60.06532241.217198.8
2.38-2.627.80.06432371.446198.4
2.62-2.998.10.05332661.261199.1
2.99-3.778.10.0433391.365199.3
3.77-507.70.03134931.268199

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 1.39→24.363 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.82
RfactorNum. reflection% reflection
Rfree0.168 1810 3.06 %
Rwork0.1333 --
obs0.1344 59132 90.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.31 Å2 / Biso mean: 16.1856 Å2 / Biso min: 5.06 Å2
Refinement stepCycle: final / Resolution: 1.39→24.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2396 0 99 320 2815
Biso mean--44.6 29.32 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052590
X-RAY DIFFRACTIONf_angle_d0.7893497
X-RAY DIFFRACTIONf_chiral_restr0.074372
X-RAY DIFFRACTIONf_plane_restr0.005449
X-RAY DIFFRACTIONf_dihedral_angle_d17.109993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3877-1.42520.24511040.17063466357073
1.4252-1.46710.20731190.143761388079
1.4671-1.51440.16171200.12413901402181
1.5144-1.56860.19631360.11214121425786
1.5686-1.63140.15831330.11454315444890
1.6314-1.70560.14981430.11554386452991
1.7056-1.79550.17311390.11414540467994
1.7955-1.90790.14971450.11194571471695
1.9079-2.05520.15891490.11454703485297
2.0552-2.26190.16421530.12174746489998
2.2619-2.58880.16091530.13734801495498
2.5888-3.26040.18731550.15234902505799
3.2604-24.3670.15971610.14775109527099

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