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- PDB-5y9i: Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) ... -

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Basic information

Entry
Database: PDB / ID: 5y9i
TitleCrystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with Co(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 / : / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
Function and homology information
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsChung, H.S. / Pemble, C.W. / Joo, S.H.
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 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Uncharacterized protein KdoO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9119
Polymers36,2391
Non-polymers6728
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-13 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.263, 59.566, 116.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 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
#4: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 398 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate (pH=4.6), 200mM Ammonium sulfate, 25% v/v PEG 4000

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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: 1.9→50 Å / Num. obs: 51868 / % possible obs: 98.3 % / Redundancy: 9.4 % / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→34.875 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.61
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1948 2405 4.98 %
Rwork0.1514 --
obs0.1536 48291 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→34.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 37 391 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062493
X-RAY DIFFRACTIONf_angle_d0.8273372
X-RAY DIFFRACTIONf_dihedral_angle_d12.1671491
X-RAY DIFFRACTIONf_chiral_restr0.054365
X-RAY DIFFRACTIONf_plane_restr0.005431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.93980.24191240.20942267X-RAY DIFFRACTION81
1.9398-1.9820.23511290.18312551X-RAY DIFFRACTION94
1.982-2.02810.21441440.17512672X-RAY DIFFRACTION97
2.0281-2.07880.22411390.16272714X-RAY DIFFRACTION99
2.0788-2.1350.20761420.15782752X-RAY DIFFRACTION100
2.135-2.19780.22251450.14192768X-RAY DIFFRACTION100
2.1978-2.26880.18241440.14392704X-RAY DIFFRACTION100
2.2688-2.34980.18541460.14422742X-RAY DIFFRACTION100
2.3498-2.44390.21781470.15022780X-RAY DIFFRACTION100
2.4439-2.55510.20841420.14912723X-RAY DIFFRACTION100
2.5551-2.68970.20071420.15062761X-RAY DIFFRACTION100
2.6897-2.85820.17671410.16282725X-RAY DIFFRACTION100
2.8582-3.07870.21781410.16172755X-RAY DIFFRACTION100
3.0787-3.38830.17561450.15272722X-RAY DIFFRACTION100
3.3883-3.87810.16921460.13232759X-RAY DIFFRACTION100
3.8781-4.88380.20461370.12322739X-RAY DIFFRACTION100
4.8838-34.88090.15661510.16742752X-RAY DIFFRACTION100

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