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- PDB-4kay: Structure of the soluble domain of Lipooligosaccharide phosphoeth... -

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Basic information

Entry
Database: PDB / ID: 4kay
TitleStructure of the soluble domain of Lipooligosaccharide phosphoethanolamine transferase A from Neisseria meningitidis - complex with Zn
ComponentsYhbX/YhjW/YijP/YjdB family protein
KeywordsTRANSFERASE / endotoxin biosynthesis / LptA / phosphoethanolamine transferase / polymyxin resistance / hydrolase / phosphotransferase phosphotransferase
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / lipopolysaccharide core region biosynthetic process / metal ion binding / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / YhbX/YhjW/YijP/YjdB family protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsVrielink, A. / Wanty, C. / Anandan, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The Structure of the Neisserial Lipooligosaccharide Phosphoethanolamine Transferase A (LptA) Required for Resistance to Polymyxin.
Authors: Wanty, C. / Anandan, A. / Piek, S. / Walshe, J. / Ganguly, J. / Carlson, R.W. / Stubbs, K.A. / Kahler, C.M. / Vrielink, A.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YhbX/YhjW/YijP/YjdB family protein
B: YhbX/YhjW/YijP/YjdB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,47510
Polymers75,8932
Non-polymers5828
Water20,1051116
1
A: YhbX/YhjW/YijP/YjdB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2385
Polymers37,9461
Non-polymers2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YhbX/YhjW/YijP/YjdB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2385
Polymers37,9461
Non-polymers2914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-149 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.068, 90.517, 91.176
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 211:279 or resseq 281:543 ) and (not element H)
211chain B and (resseq 211:279 or resseq 281:543 ) and (not element H)

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Components

#1: Protein YhbX/YhjW/YijP/YjdB family protein


Mass: 37946.430 Da / Num. of mol.: 2 / Fragment: Periplasmic Soluble Domain (unp residues 210-544)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: NMB / Gene: NMB1638 / Plasmid: pCMK527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DD94, phosphatidylglycerophosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23-26% PEG 8K, 100 mM ammonium sulfate, 100 mM HEPES, 15 mM n-dodecyl-N,N-dimethylamine- N-oxide (DDAO), VAPOR DIFFUSION, HANGING DROP, temperature 293K
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2011
RadiationMonochromator: undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.78→19.8 Å / Num. all: 67558 / Num. obs: 67558 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.99-2.130.3211100
1.88-1.991100
1.78-1.88195.2
1.88-1.991100
1.99-2.131100
2.13-2.31100
2.3-2.521100
2.52-2.811100
2.81-3.251100
3.25-3.981100
3.98-5.631100
5.63-19.8197.7

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAV

4kav


Resolution: 1.781→19.799 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 3361 5.06 %
Rwork0.1493 --
obs0.1514 66393 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0692 Å20 Å2-0 Å2
2--10.4433 Å20 Å2
3----5.3741 Å2
Refinement stepCycle: LAST / Resolution: 1.781→19.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 16 1116 6414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155675
X-RAY DIFFRACTIONf_angle_d1.5237747
X-RAY DIFFRACTIONf_dihedral_angle_d14.7442165
X-RAY DIFFRACTIONf_chiral_restr0.094856
X-RAY DIFFRACTIONf_plane_restr0.0081025
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2646X-RAY DIFFRACTIONPOSITIONAL
12B2646X-RAY DIFFRACTIONPOSITIONAL0.135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7809-1.80630.25411270.19512233X-RAY DIFFRACTION85
1.8063-1.83320.25461200.19542441X-RAY DIFFRACTION92
1.8332-1.86180.28371670.19392498X-RAY DIFFRACTION95
1.8618-1.89230.2271540.17232638X-RAY DIFFRACTION100
1.8923-1.9250.20921380.17212653X-RAY DIFFRACTION100
1.925-1.95990.19781300.1672630X-RAY DIFFRACTION100
1.9599-1.99760.22411670.16772620X-RAY DIFFRACTION100
1.9976-2.03830.21391490.15972649X-RAY DIFFRACTION99
2.0383-2.08260.19791250.15572681X-RAY DIFFRACTION100
2.0826-2.1310.21721400.1512641X-RAY DIFFRACTION99
2.131-2.18420.1831490.14452653X-RAY DIFFRACTION100
2.1842-2.24320.15931460.1352648X-RAY DIFFRACTION100
2.2432-2.30910.17791540.13552626X-RAY DIFFRACTION99
2.3091-2.38350.20391340.14012666X-RAY DIFFRACTION99
2.3835-2.46860.19971340.13972656X-RAY DIFFRACTION99
2.4686-2.56720.18761400.14162688X-RAY DIFFRACTION99
2.5672-2.68380.20261580.14352624X-RAY DIFFRACTION99
2.6838-2.82490.18591440.14722652X-RAY DIFFRACTION99
2.8249-3.00130.18811130.14352678X-RAY DIFFRACTION99
3.0013-3.23210.18631170.14872687X-RAY DIFFRACTION98
3.2321-3.55570.19561290.14862689X-RAY DIFFRACTION98
3.5557-4.06630.17461390.13672667X-RAY DIFFRACTION98
4.0663-5.10850.14771270.12562692X-RAY DIFFRACTION96
5.1085-19.80.1531600.16492722X-RAY DIFFRACTION95

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