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- PDB-2xci: Membrane-embedded monofunctional glycosyltransferase WaaA of Aqui... -

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Basic information

Entry
Database: PDB / ID: 2xci
TitleMembrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, substrate-free form
Components3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
KeywordsTRANSFERASE / KDTA / GSEA / GLYCOSYLTRANSFERASE SUPERFAMILY B / GT-B
Function / homology
Function and homology information


lipid IVA 3-deoxy-D-manno-octulosonic acid transferase / Kdo transferase activity / lipopolysaccharide core region biosynthetic process / lipid A biosynthetic process / transferase activity / plasma membrane
Similarity search - Function
3-Deoxy-D-manno-octulosonic-acid transferase, N-terminal domain / 3-deoxy-D-manno-octulosonic-acid transferase, N-terminal / 3-deoxy-D-manno-octulosonic-acid transferase, N-terminal domain superfamily / 3-deoxy-D-manno-octulosonic acid transferase / 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase) / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / NICKEL (II) ION / 3-deoxy-D-manno-octulosonic acid transferase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsSchmidt, H. / Hansen, G. / Hilgenfeld, R. / Mamat, U. / Mesters, J.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and Mechanistic Analysis of the Membrane-Embedded Glycosyltransferase Waaa Required for Lipopolysaccharide Synthesis.
Authors: Schmidt, H. / Hansen, G. / Singh, S. / Hanuszkiewicz, A. / Lindner, B. / Fukase, K. / Woodard, R.W. / Holst, O. / Hilgenfeld, R. / Mamat, U. / Mesters, J.R.
#1: Journal: J.Biol.Chem. / Year: 2009
Title: Waaa of the Hyperthermophilic Bacterium Aquifex Aeolicus is a Monofunctional 3-Deoxy-D-Manno-Oct-2- Ulosonic Acid Transferase Involved in Lipopolysaccharide Biosynthesis.
Authors: Mamat, U. / Schmidt, H. / Munoz, E. / Lindner, B. / Fukase, K. / Hanuszkiewicz, A. / Wu, J. / Meredith, T.C. / Woodard, R.W. / Hilgenfeld, R. / Mesters, J.R. / Holst, O.
History
DepositionApr 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references / Non-polymer description / Version format compliance
Revision 1.2May 2, 2012Group: Other
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
B: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
C: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
D: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,30330
Polymers173,1154
Non-polymers2,18826
Water4,468248
1
A: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
C: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,82217
Polymers86,5582
Non-polymers1,26415
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-65.6 kcal/mol
Surface area29530 Å2
MethodPISA
2
B: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
D: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,48213
Polymers86,5582
Non-polymers92411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-53 kcal/mol
Surface area29720 Å2
MethodPISA
3
A: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,10910
Polymers43,2791
Non-polymers8309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5005
Polymers43,2791
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7137
Polymers43,2791
Non-polymers4356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9818
Polymers43,2791
Non-polymers7027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.500, 45.820, 144.070
Angle α, β, γ (deg.)90.00, 97.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE / KDO-TRANSFERASE


Mass: 43278.785 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Strain: AQ_326 / Plasmid: PUM216 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SI-216 / References: UniProt: O66663

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Non-polymers , 6 types, 274 molecules

#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Description: DERIVATIVE USED FOR THIS EXPERIMENT IS K3IRCL6 POTASSIUM HEXACHLORO IRIDATE (III)
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND ...Details: HANGING-DROP VAPOR-DIFFUSION TECHNIQUE MIXING EQUAL VOLUMES OF PROTEIN SOLUTION (10-15 MG/ML, 25 MM TRIS-HCL, PH 8.7, 0.1 M NACL, 10% GLYCEROL, 2 MM CYMAL-6, 5 MM 2-MERCAPTOETHANOL) AND RESERVOIR (100 MM TRIS-HCL, PH 8.5, 35-40% (V/V) PEG 400, 200 MM NA-CITRATE, 50 MM 2-MERCAPTOETHANOL)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.255
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.255 Å / Relative weight: 1
ReflectionResolution: 2→29.85 Å / Num. obs: 115974 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 37.72 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2→29.854 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2539 5821 5 %
Rwork0.2071 --
obs0.2095 115974 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.247 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3208 Å20 Å2-0.5529 Å2
2--19.052 Å20 Å2
3----13.7312 Å2
Refinement stepCycle: LAST / Resolution: 2→29.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11499 0 110 248 11857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811849
X-RAY DIFFRACTIONf_angle_d1.1215846
X-RAY DIFFRACTIONf_dihedral_angle_d17.084516
X-RAY DIFFRACTIONf_chiral_restr0.0781751
X-RAY DIFFRACTIONf_plane_restr0.0051950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.36211950.31413429X-RAY DIFFRACTION94
2.0227-2.04650.34442210.30493505X-RAY DIFFRACTION96
2.0465-2.07150.33691590.30953615X-RAY DIFFRACTION96
2.0715-2.09770.35581790.29943623X-RAY DIFFRACTION98
2.0977-2.12530.35671770.27663566X-RAY DIFFRACTION98
2.1253-2.15440.30592260.2723611X-RAY DIFFRACTION98
2.1544-2.18520.30181680.25863670X-RAY DIFFRACTION98
2.1852-2.21780.29611760.23713607X-RAY DIFFRACTION99
2.2178-2.25240.29012000.22813605X-RAY DIFFRACTION99
2.2524-2.28930.28491830.22753722X-RAY DIFFRACTION99
2.2893-2.32880.27871750.2193630X-RAY DIFFRACTION99
2.3288-2.37110.27722140.24093605X-RAY DIFFRACTION99
2.3711-2.41670.32412020.23533687X-RAY DIFFRACTION99
2.4167-2.4660.26881910.22173568X-RAY DIFFRACTION99
2.466-2.51960.28542230.21473706X-RAY DIFFRACTION99
2.5196-2.57820.2961900.22263654X-RAY DIFFRACTION99
2.5782-2.64260.2571980.22783648X-RAY DIFFRACTION99
2.6426-2.7140.31541870.22923716X-RAY DIFFRACTION100
2.714-2.79380.31052050.22493642X-RAY DIFFRACTION100
2.7938-2.88390.29951930.22033753X-RAY DIFFRACTION100
2.8839-2.98690.31271840.23363681X-RAY DIFFRACTION100
2.9869-3.10640.28161670.2293761X-RAY DIFFRACTION100
3.1064-3.24760.26591890.2173724X-RAY DIFFRACTION100
3.2476-3.41860.25452050.20483708X-RAY DIFFRACTION100
3.4186-3.63240.23521930.20123702X-RAY DIFFRACTION100
3.6324-3.91230.24852050.183764X-RAY DIFFRACTION100
3.9123-4.3050.20162080.16773728X-RAY DIFFRACTION100
4.305-4.92550.19151930.15013792X-RAY DIFFRACTION100
4.9255-6.19650.21882020.17653804X-RAY DIFFRACTION100
6.1965-29.85730.19072130.18013927X-RAY DIFFRACTION99
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)
10.9742-0.1625-1.31030.5739-0.16132.9063-0.0739-0.4544-0.0877-0.0120.12130.00270.1289-0.2235-0.05110.14060.0254-0.02370.43580.04450.208617.17669.859834.8673
21.3421-0.3314-0.7560.65780.50822.59-0.0937-0.5985-0.09350.05720.09090.02590.2457-0.37220.08820.17520.06740.00980.45270.02820.2264-49.3788-9.029832.2967
31.0249-0.25880.72930.66690.01452.9022-0.0972-0.50860.10370.05760.1541-0.0231-0.14750.397-0.06150.16250.02870.00810.5444-0.06330.239249.014613.412634.9981
41.577-0.49980.76340.8669-0.87212.892-0.1412-0.61150.0680.09080.0837-0.0365-0.26870.2640.07390.18660.0654-0.01880.4196-0.03580.237-17.4241-14.326632.4866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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