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- PDB-8ees: Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransfer... -

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Basic information

Entry
Database: PDB / ID: 8ees
TitleCrystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Klebsiella pneumoniae
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / HYDROLASE
Function / homology
Function and homology information


3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide biosynthetic process / cytoplasm
Similarity search - Function
3-deoxy-D-manno-octulosonate cytidylyltransferase / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of 3-deoxy-manno-octulosonate cytidylyltransferase from Klebsiella pneumoniae
Authors: Liu, L. / Seibold, S. / Battaile, K.P. / Lovell, S.
History
DepositionSep 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)56,1282
Polymers56,1282
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-20 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.140, 78.098, 81.991
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-deoxy-manno-octulosonate cytidylyltransferase / CMP-2-keto-3-deoxyoctulosonic acid synthase / CKS / CMP-KDO synthase


Mass: 28063.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: kdsB, KPHS_18250 / Plasmid: KlpnC.01328.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GMB7, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% PEG 4000, 0.1 M sodium acetate, pH 4.0, KlpnC.01328.a.B1.PW39074 at 14 mg/mL. Tray: plate Liu-Limbro 20220712 D3, well H8 drop 3, Puck: PSL0214, Cryo: 33% PEG 4000, 0.1 M sodium acetate, pH 4.8.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 11, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→81.99 Å / Num. obs: 15381 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 56.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Net I/σ(I): 14.1 / Num. measured all: 56853 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.563.50.312383011090.950.1940.3683.399.9
11.18-81.993.30.0346111840.9990.0210.0425.998.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
MOLREPphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VH1

1vh1


Resolution: 2.5→22.39 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.1 / Stereochemistry target values: ML
Details: Very anisotropic data that were cut to 2.5A resolution. The beta angle is close to 90 degrees but the data scaled poorly in an orthorhombic lattice.
RfactorNum. reflection% reflection
Rfree0.2725 786 5.13 %
Rwork0.2404 14536 -
obs0.2421 15322 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 209.38 Å2 / Biso mean: 94.1017 Å2 / Biso min: 28.35 Å2
Refinement stepCycle: final / Resolution: 2.5→22.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 0 16 3409
Biso mean---48.79 -
Num. residues----447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.660.38051100.33882385249599
2.66-2.860.34291200.317724352555100
2.86-3.150.30971810.288323712552100
3.15-3.60.2914970.277724682565100
3.6-4.530.24791700.212923942564100
4.53-22.390.24561080.20472483259199
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)
14.3187-1.32370.33424.3426-2.01035.4633-0.05921.2253-0.1647-0.2729-0.54951.0250.0807-0.25830.43140.6574-0.07980.08961.1041-0.56031.0107-16.9829-0.4214-50.9106
22.3341.28232.15620.80111.19862.0523-0.45040.744-0.77830.0543-0.10150.2761.35540.3613-0.27311.1136-0.07720.35220.7179-0.43241.058-14.7883-2.8074-37.3154
38.66841.5099-3.6365.74790.3776.5543-0.216-0.28980.58110.4349-0.0013-0.3749-0.09590.71360.18990.286-0.004-0.14380.50570.03020.392-11.640217.4484-22.7032
43.0298-2.0349-1.21831.76891.45981.3996-0.79741.3833-0.405-0.1892-0.3420.54240.7937-0.94810.20530.651-0.33230.0271.0121-0.30970.6714-18.51895.5906-33.9395
55.26010.35690.59921.6986-0.03182.9045-0.8131-0.91850.30910.41310.2833-0.19740.52541.97380.18350.92330.2236-0.00392.08810.30650.6946-21.658711.727611.2682
68.26120.0052-3.93573.53540.30294.3141-0.5191-1.0368-0.29950.41810.1572-0.03150.38460.79490.16340.38790.1155-0.07540.61440.05390.3581-20.766512.7509-11.1131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 76 )A2 - 76
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 129 )A77 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 178 )A130 - 178
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 247 )A179 - 247
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 118 )B2 - 118
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 226 )B119 - 226

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