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- PDB-4kav: Crystal Structure of the soluble domain of Lipooligosaccharide ph... -

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Basic information

Entry
Database: PDB / ID: 4kav
TitleCrystal Structure of the soluble domain of Lipooligosaccharide phosphoethanolamine transferase A from Neisseria meningitidis
ComponentsYhbX/YhjW/YijP/YjdB family protein
KeywordsTRANSFERASE / endotoxin biosynthesis / LptA / phosphoethanolamine transferase / polymyxin resistance / hydrolase / phosphotransferase / phosphotransfer reaction
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
COPPER (II) ION / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / PHOSPHATE ION / YhbX/YhjW/YijP/YjdB family protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.433 Å
AuthorsVrielink, A. / Wanty, C.
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 24, 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: YhbX/YhjW/YijP/YjdB family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7708
Polymers38,2751
Non-polymers4967
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.696, 44.923, 50.179
Angle α, β, γ (deg.)70.26, 69.36, 61.13
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 38274.691 Da / Num. of mol.: 1 / 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: lpta, NMB1638 / Plasmid: pCMK527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7DD94, phosphatidylglycerophosphatase

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Non-polymers , 7 types, 500 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.06 Å3/Da / Density % sol: 40.42 %
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), pH 7.5-8.0, 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: 0.97884, 0.9686
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: undulator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.96861
ReflectionResolution: 1.433→20 Å / Num. obs: 49289 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.43-1.51166.6
1.51-1.6194.7
1.6-1.71195.6
1.71-1.85196.2
1.85-2.02196.6
2.02-2.26197.3
2.26-2.61197.9
2.61-3.2198.3
3.2-4.53198.6
4.53-19.26198.1

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.433→19.255 Å / SU ML: 0.11 / σ(F): 1.96 / Phase error: 14.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1565 2653 5.11 %
Rwork0.1158 --
obs0.1178 49289 92.25 %
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--0.7524 Å2-1.4426 Å2-0.91 Å2
2--0.4466 Å21.0471 Å2
3---0.3059 Å2
Refinement stepCycle: LAST / Resolution: 1.433→19.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 24 493 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0262993
X-RAY DIFFRACTIONf_angle_d1.4114103
X-RAY DIFFRACTIONf_dihedral_angle_d14.4621150
X-RAY DIFFRACTIONf_chiral_restr0.083450
X-RAY DIFFRACTIONf_plane_restr0.007543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4328-1.45890.3113830.2561430X-RAY DIFFRACTION51
1.4589-1.48690.19281040.15921947X-RAY DIFFRACTION69
1.4869-1.51720.18961160.13342421X-RAY DIFFRACTION86
1.5172-1.55020.18691340.11742682X-RAY DIFFRACTION95
1.5502-1.58630.17721410.11182635X-RAY DIFFRACTION95
1.5863-1.62590.17011500.10522703X-RAY DIFFRACTION95
1.6259-1.66990.17451550.10462701X-RAY DIFFRACTION95
1.6699-1.7190.14921450.09912655X-RAY DIFFRACTION96
1.719-1.77440.16391620.10062682X-RAY DIFFRACTION96
1.7744-1.83780.14791540.1052689X-RAY DIFFRACTION96
1.8378-1.91130.16681560.10452703X-RAY DIFFRACTION96
1.9113-1.99820.14861460.10132706X-RAY DIFFRACTION97
1.9982-2.10340.15471420.10622735X-RAY DIFFRACTION97
2.1034-2.2350.14611490.10372734X-RAY DIFFRACTION97
2.235-2.40730.1431490.10512745X-RAY DIFFRACTION98
2.4073-2.6490.16241490.11352752X-RAY DIFFRACTION98
2.649-3.0310.15661480.12682754X-RAY DIFFRACTION98
3.031-3.81390.14851270.12012793X-RAY DIFFRACTION98
3.8139-19.25690.13121430.12762791X-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)
10.8803-1.26530.60965.8481-1.59271.43220.16630.0377-0.0754-0.6683-0.1877-0.0870.21080.15910.02940.09770.0023-0.00920.1052-0.0220.0711.0652-2.5937-20.4402
20.39540.0230.04210.238-0.1730.858-0.0070.0067-0.01070.01020.01260.02270.0493-0.0910.00180.0178-0.00510.00180.02170.00010.02513.367-0.76782.619
36.5437-0.4669-0.52744.9956-0.45424.5583-0.0138-0.3395-0.79470.1766-0.00150.25120.40.1330.00840.10430.04590.03770.10360.00390.161212.55-14.8148-12.5881
41.17080.13670.99420.33770.21872.06370.0740.0225-0.10840.01920.0155-0.06490.10640.3-0.05830.0304-0.00040.00790.08350.00050.048418.84840.1757-4.9393
55.2491-0.71040.50954.00170.91592.3937-0.0527-0.1832-0.01660.36930.0532-0.23830.02350.3061-0.01590.0768-0.016-0.01780.0986-0.00460.062522.87074.142613.6405
60.2815-0.48791.12881.3466-2.57975.2979-0.08020.07360.0613-0.0123-0.1404-0.1827-0.17230.32610.17030.0748-0.0347-0.0050.07830.00620.069919.019313.3395-3.0108
70.52880.206-0.37420.4116-0.07121.3213-0.0008-0.1062-0.02950.0919-0.0419-0.04330.05030.07570.01730.03270.0002-0.01280.03110.00290.021311.4045-0.110118.0979
80.6747-0.25980.28881.842-0.47861.42340.0383-0.02270.0150.1715-0.03170.1331-0.1052-0.0203-0.05390.0143-0.01060.0128-0.0128-0.00250.00136.29074.04415.3425
91.47770.00110.2651.7250.17571.01940.08520.0062-0.1675-0.065-0.01020.11860.322-0.0294-0.0670.0967-0.0155-0.00010.0539-0.00730.04072.7047-12.00128.9034
100.63050.0123-0.20940.8773-0.28531.89920.01360.1280.1187-0.03840.02570.1858-0.083-0.257-0.1340.02350.01850.00330.02650.03940.0549-4.167712.5781-3.5442
110.9057-0.3522-0.2780.78470.06621.09330.0186-0.00780.0318-0.02050.03750.0532-0.0814-0.1145-0.04470.0127-0.0061-0.01210.0607-0.02070.0428-0.79060.4889-6.4991
122.5211-0.2876-0.70332.50690.982.5813-0.00150.22380.0479-0.22170.01010.1016-0.0299-0.1709-0.00420.0667-0.0118-0.02340.10410.00640.0473-3.25831.5834-13.8495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 210:227)
2X-RAY DIFFRACTION2(chain A and resid 228:296)
3X-RAY DIFFRACTION3(chain A and resid 297:305)
4X-RAY DIFFRACTION4(chain A and resid 306:343)
5X-RAY DIFFRACTION5(chain A and resid 344:356)
6X-RAY DIFFRACTION6(chain A and resid 357:371)
7X-RAY DIFFRACTION7(chain A and resid 372:432)
8X-RAY DIFFRACTION8(chain A and resid 433:462)
9X-RAY DIFFRACTION9(chain A and resid 463:481)
10X-RAY DIFFRACTION10(chain A and resid 482:502)
11X-RAY DIFFRACTION11(chain A and resid 503:523)
12X-RAY DIFFRACTION12(chain A and resid 524:543)

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