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- PDB-5k8c: X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxi... -

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Basic information

Entry
Database: PDB / ID: 5k8c
TitleX-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis
Components3-deoxy-alpha-D-manno-octulosonate 8-oxidase
KeywordsTRANSFERASE / Group III alcohol dehydrogenase / 8-amino-3 / 8-dideoxy-d-manno-octulosonic acid / deoxy sugar
Function / homology
Function and homology information


3-deoxy-alpha-D-manno-octulosonate 8-oxidase / lipopolysaccharide biosynthetic process / alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / 3-deoxy-alpha-D-manno-octulosonate 8-oxidase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHolden, H.M. / Thoden, J.B. / Zachman-Brockmeyer, T.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid.
Authors: Zachman-Brockmeyer, T.R. / Thoden, J.B. / Holden, H.M.
History
DepositionMay 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7228
Polymers39,6711
Non-polymers1,0527
Water7,891438
1
A: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase
hetero molecules

A: 3-deoxy-alpha-D-manno-octulosonate 8-oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,44516
Polymers79,3412
Non-polymers2,10414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_467y-1,x+1,-z+21
Buried area7950 Å2
ΔGint-171 kcal/mol
Surface area27000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.594, 107.594, 149.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

21A-785-

HOH

31A-868-

HOH

41A-909-

HOH

51A-930-

HOH

61A-934-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-deoxy-alpha-D-manno-octulosonate 8-oxidase


Mass: 39670.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: kdnB, SO_2477 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8EEB0, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase

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Non-polymers , 6 types, 445 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 7-9% PEG-8000, 100 mM homopipes, 1 M tetramethylammonium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→93.18 Å / Num. obs: 44036 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RF7

3rf7


Resolution: 1.85→93.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.051 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21811 2218 5 %RANDOM
Rwork0.17851 ---
obs0.18052 41818 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.85→93.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 61 438 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192916
X-RAY DIFFRACTIONr_bond_other_d0.0010.022754
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.9823957
X-RAY DIFFRACTIONr_angle_other_deg1.08536367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57725122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76115500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.318159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7291.651437
X-RAY DIFFRACTIONr_mcbond_other1.7281.651436
X-RAY DIFFRACTIONr_mcangle_it2.4222.4671796
X-RAY DIFFRACTIONr_mcangle_other2.4232.4681797
X-RAY DIFFRACTIONr_scbond_it2.8711.9641479
X-RAY DIFFRACTIONr_scbond_other2.8651.9641479
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2582.832159
X-RAY DIFFRACTIONr_long_range_B_refined6.24815.1153768
X-RAY DIFFRACTIONr_long_range_B_other6.24715.123769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 149 -
Rwork0.318 3021 -
obs--98.82 %

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