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

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Basic information

Entry
Database: PDB / ID: 2xcu
TitleMembrane-embedded monofunctional glycosyltransferase WaaA of Aquifex aeolicus, complex with CMP
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 / CYTIDINE-5'-MONOPHOSPHATE / CITRIC ACID / 3-deoxy-D-manno-octulosonic acid transferase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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 / Version format compliance
Revision 1.2May 2, 2012Group: Other
Revision 1.3Sep 28, 2016Group: Structure summary
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)176,67022
Polymers173,1154
Non-polymers3,55518
Water2,108117
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)88,41311
Polymers86,5582
Non-polymers1,8569
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-17.9 kcal/mol
Surface area29690 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)88,25611
Polymers86,5582
Non-polymers1,6999
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-16.9 kcal/mol
Surface area29650 Å2
MethodPISA
3
A: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4636
Polymers43,2791
Non-polymers1,1845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1466
Polymers43,2791
Non-polymers8675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9505
Polymers43,2791
Non-polymers6724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: 3-DEOXY-D-MANNO-2-OCTULOSONIC ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1115
Polymers43,2791
Non-polymers8324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.770, 44.670, 143.640
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12B
22A
32C
42D
13C
23A
33B
43D
14D
24A
34B
44C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 1 - 352 / Label seq-ID: 22 - 373

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
31CC
41DD
12BB
22AA
32CC
42DD
13CC
23AA
33BB
43DD
14DD
24AA
34BB
44CC

NCS ensembles :
ID
1
2
3
4

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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, 135 molecules

#2: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: NONE
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); SOAKING CRYSTALS IN 100 MM TRIS-HCL (PH 8.5), 36% (V/V) PEG 400, 200 MM NA-CITRATE AND 10 MM CMP FOR FOUR DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jan 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 2.42→31.85 Å / Num. obs: 62789 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 47.57 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.3
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 6.8 / % possible all: 88.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCI

2xci


Resolution: 2.42→31.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 17.569 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.493 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25087 3139 5 %RANDOM
Rwork0.20236 ---
obs0.20478 59636 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.993 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å2-0.3 Å2
2--6.95 Å20 Å2
3----4.43 Å2
Refinement stepCycle: LAST / Resolution: 2.42→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11488 0 230 117 11835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02211974
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5872.00416051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55551406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34323.621486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.634152342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8151560
X-RAY DIFFRACTIONr_chiral_restr0.1040.21770
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218560
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7221.57006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.407211372
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02734968
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5014.54679
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Number: 2867 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Amedium positional0.30.5
12Bmedium positional0.390.5
13Cmedium positional0.270.5
14Dmedium positional0.370.5
22Amedium positional0.390.5
21Bmedium positional0.30.5
23Cmedium positional0.270.5
24Dmedium positional0.370.5
32Amedium positional0.270.5
33Bmedium positional0.30.5
31Cmedium positional0.390.5
34Dmedium positional0.370.5
42Amedium positional0.370.5
43Bmedium positional0.30.5
44Cmedium positional0.390.5
41Dmedium positional0.270.5
11Amedium thermal0.312
12Bmedium thermal0.32
13Cmedium thermal0.292
14Dmedium thermal0.32
22Amedium thermal0.32
21Bmedium thermal0.312
23Cmedium thermal0.292
24Dmedium thermal0.32
32Amedium thermal0.292
33Bmedium thermal0.312
31Cmedium thermal0.32
34Dmedium thermal0.32
42Amedium thermal0.32
43Bmedium thermal0.312
44Cmedium thermal0.32
41Dmedium thermal0.292
LS refinement shellResolution: 2.419→2.482 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 223 -
Rwork0.279 3841 -
obs--84.81 %
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)
11.7243-0.5282-0.5990.71590.0331.5523-0.0683-0.1825-0.0553-0.07790.0602-0.05550.1445-0.16250.00810.1108-0.0086-0.00340.05830.01490.143318.20237.234117.8605
22.4646-0.70221.14591.0401-0.44774.4487-0.0274-0.2254-0.0539-0.05870.0873-0.0019-0.16770.0821-0.060.03210.04050.01350.14820.02580.007716.16712.486653.5445
31.5392-0.8753-1.12490.93350.79412.9368-0.06570.0279-0.0305-0.0154-0.0572-0.01540.0383-0.45710.12290.11-0.0094-0.00160.0926-0.01440.1349-48.3882-10.514815.3345
41.9148-0.68091.5150.6896-1.03736.23060.0022-0.32120.0198-0.1474-0.0627-0.0380.1285-0.26520.06050.05090.0620.01970.233-0.02110.0533-49.0339-5.924150.9305
51.8926-0.86930.24320.579-0.17591.7001-0.092-0.25070.0955-0.06170.09970.022-0.15140.2052-0.00770.1172-0.0074-0.0090.0674-0.01860.159747.693215.508117.9678
62.7964-0.492-1.10850.5760.48264.8066-0.0871-0.51020.05070.03170.15530.00520.0170.1356-0.06820.04070.1025-0.02030.2939-0.04360.040549.478210.208753.6818
71.7266-0.71381.15981.0672-0.99623.1607-0.031-0.0095-0.0174-0.1068-0.05930.0579-0.00940.45770.09030.1059-0.00070.00990.09490.00980.126-17.5991-11.233715.4353
83.1691-1.32-1.2751.46950.62314.7875-0.1761-0.5581-0.0190.01020.1050.04590.05710.11280.07110.03590.088-0.00960.25330.01620.0533-17.6731-17.769351.0875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION1A337 - 352
3X-RAY DIFFRACTION2A176 - 336
4X-RAY DIFFRACTION3B1 - 164
5X-RAY DIFFRACTION3B337 - 352
6X-RAY DIFFRACTION4B176 - 336
7X-RAY DIFFRACTION5C1 - 164
8X-RAY DIFFRACTION5C337 - 352
9X-RAY DIFFRACTION6C176 - 336
10X-RAY DIFFRACTION7D1 - 164
11X-RAY DIFFRACTION7D337 - 352
12X-RAY DIFFRACTION8D176 - 336

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