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- PDB-5fgn: Integral membrane protein lipooligosaccharide phosphoethanolamine... -

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Basic information

Entry
Database: PDB / ID: 5fgn
TitleIntegral membrane protein lipooligosaccharide phosphoethanolamine transferase A (EptA) from Neisseria meningitidis
Componentslipooligosaccharide phosphoethanolamine transferase A
KeywordsTRANSFERASE / HYDROLASE / Endotoxin Biosynthesis / EptA / Membrane protein / Phosphoethanolamine transferase / Polymixin Resistance / Phosphotransferase
Function / homology
Function and homology information


phosphotransferase activity, phosphate group as acceptor / transferase activity, transferring phosphorus-containing groups / sulfuric ester hydrolase activity / lipopolysaccharide core region biosynthetic process / membrane => GO:0016020 / 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
YhbX/YhjW/YijP/YjdB family protein / YhbX/YhjW/YijP/YjdB family protein
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsAnandan, A. / Vrielink, A.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP 1003697 Australia
National Health and Medical Research Council (NHMRC, Australia)APP 1078642 Australia
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of a lipid A phosphoethanolamine transferase suggests how conformational changes govern substrate binding.
Authors: Anandan, A. / Evans, G.L. / Condic-Jurkic, K. / O'Mara, M.L. / John, C.M. / Phillips, N.J. / Jarvis, G.A. / Wills, S.S. / Stubbs, K.A. / Moraes, I. / Kahler, C.M. / Vrielink, A.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipooligosaccharide phosphoethanolamine transferase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1614
Polymers62,2921
Non-polymers8683
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)187.285, 187.285, 205.125
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-777-

HOH

21A-817-

HOH

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Components

#1: Protein lipooligosaccharide phosphoethanolamine transferase A / EptA


Mass: 62292.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C terminal Histag
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: NMB1638 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: E3D1H8, UniProt: Q7DD94*PLUS
#2: Sugar ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 7.22 Å3/Da / Density % sol: 82.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium Sulphate, Hepes, Beta octylglucoside / 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: Aug 9, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→138.308 Å / Num. all: 47424 / Num. obs: 47424 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 53.48 Å2 / Rpim(I) all: 0.086 / Rrim(I) all: 0.278 / Rsym value: 0.264 / Net I/av σ(I): 2.375 / Net I/σ(I): 9.3 / Num. measured all: 487530
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.75-2.910.42.3660.37079468040.7622.4882.3661.3100
2.9-3.0710.41.6170.56759564880.521.71.6171.9100
3.07-3.2910.40.9660.86356461140.3111.0160.9663100
3.29-3.5510.40.5051.55903056890.1630.5310.5055.5100
3.55-3.8910.30.2742.85431952530.0890.2890.2749.2100
3.89-4.3510.30.164.84911947700.0520.1680.1613.9100
4.35-5.0210.20.1325.64322042300.0430.1380.13218100
5.02-6.1510.10.1474.93637836050.0480.1550.14716.4100
6.15-8.79.80.0749.92796728420.0240.0780.07421.9100
8.7-46.8219.50.0344.51554416290.0130.0370.03434.499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALA3.3.20data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KAV

4kav


Resolution: 2.75→46.821 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 2401 5.07 %Random selection
Rwork0.2142 44992 --
obs0.2155 47393 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.36 Å2 / Biso mean: 52.2177 Å2 / Biso min: 35.6 Å2
Refinement stepCycle: final / Resolution: 2.75→46.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 84 126 4463
Biso mean--64.43 51.98 -
Num. residues----536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014417
X-RAY DIFFRACTIONf_angle_d1.0335998
X-RAY DIFFRACTIONf_chiral_restr0.047689
X-RAY DIFFRACTIONf_plane_restr0.004754
X-RAY DIFFRACTIONf_dihedral_angle_d14.9281576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.84830.35122300.303144424672100
2.8483-2.96230.29192660.2843954661100
2.9623-3.09710.3042170.263444524669100
3.0971-3.26040.30122300.24244774707100
3.2604-3.46460.21832530.206844404693100
3.4646-3.7320.23372310.202944944725100
3.732-4.10730.23722360.196344974733100
4.1073-4.70120.20982400.178845114751100
4.7012-5.92110.20192610.189745404801100
5.9211-46.8280.24642370.2254744498199
Refinement TLS params.Method: refined / Origin x: 35.5297 Å / Origin y: -16.6605 Å / Origin z: -24.3702 Å
111213212223313233
T0.5077 Å20.0442 Å20.0596 Å2-0.5887 Å2-0.0245 Å2--0.5052 Å2
L0.4738 °2-0.2629 °2-0.1692 °2-0.7947 °20.3346 °2--0.5437 °2
S-0.0037 Å °0.1023 Å °-0.0775 Å °-0.1644 Å °-0.0094 Å °-0.1383 Å °0.0869 Å °0.1559 Å °0.0114 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 543
2X-RAY DIFFRACTION1allF1 - 137
3X-RAY DIFFRACTION1allF138
4X-RAY DIFFRACTION1allE1
5X-RAY DIFFRACTION1allC4912
6X-RAY DIFFRACTION1allB1

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