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- PDB-5xhq: Apolipoprotein N-acyl Transferase -

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Basic information

Entry
Database: PDB / ID: 5xhq
TitleApolipoprotein N-acyl Transferase
ComponentsApolipoprotein N-acyltransferase
KeywordsTRANSFERASE / nitrilase post-lipidation lipoprotein
Function / homology
Function and homology information


apolipoprotein N-acyltransferase / N-acyltransferase activity / lipoprotein biosynthetic process / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
Apolipoprotein N-acyltransferase, N-terminal / Apolipoprotein N-acyltransferase N-terminal domain / Apolipoprotein N-acyltransferase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Apolipoprotein N-acyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.587 Å
AuthorsYingzhi, X. / Yong, X. / Guangyuan, L. / Fei, S.
Funding support China, 3items
OrganizationGrant numberCountry
the Ministry of Science and Technology (China)2014CB910104 to XCZ China
the Chinese Academy of SciencesXDB080203 to XCZ and FS China
National Natural Science Foundation of China31470745 to XCZ China
CitationJournal: Nat Commun / Year: 2017
Title: Crystal structure of E. coli apolipoprotein N-acyl transferase
Authors: Lu, G. / Xu, Y. / Zhang, K. / Xiong, Y. / Li, H. / Cui, L. / Wang, X. / Lou, J. / Zhai, Y. / Sun, F. / Zhang, X.C.
History
DepositionApr 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 22, 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

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Assembly

Deposited unit
A: Apolipoprotein N-acyltransferase
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,41112
Polymers114,2482
Non-polymers2,16310
Water37821
1
A: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8194
Polymers57,1241
Non-polymers6953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19680 Å2
MethodPISA
2
B: Apolipoprotein N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5928
Polymers57,1241
Non-polymers1,4687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.869, 134.094, 135.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Apolipoprotein N-acyltransferase / ALP N-acyltransferase / Copper homeostasis protein CutE


Mass: 57124.234 Da / Num. of mol.: 2 / Fragment: UNP residues 1-508 / Mutation: C62G, A283V, A377V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lnt, cutE, b0657, JW0654 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: P23930, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris-HCl (pH 7.5) and 26% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.587→40.4 Å / Num. obs: 51623 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.665 / Num. unique obs: 1457 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-20002.2.0data reduction
HKL-20002.2.0data scaling
PHENIXdev_1819phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMS

1ems


Resolution: 2.587→40.364 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 2138 5.08 %
Rwork0.2327 --
obs0.2355 42099 80.57 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.587→40.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7642 0 121 21 7784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0137979
X-RAY DIFFRACTIONf_angle_d1.54910890
X-RAY DIFFRACTIONf_dihedral_angle_d15.4432826
X-RAY DIFFRACTIONf_chiral_restr0.0591249
X-RAY DIFFRACTIONf_plane_restr0.011348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5871-2.64730.2833350.242677X-RAY DIFFRACTION21
2.6473-2.71340.3919710.23161214X-RAY DIFFRACTION37
2.7134-2.78680.3333820.23171586X-RAY DIFFRACTION49
2.7868-2.86880.30321040.23781966X-RAY DIFFRACTION60
2.8688-2.96130.27771150.25272303X-RAY DIFFRACTION70
2.9613-3.06720.31151610.262632X-RAY DIFFRACTION81
3.0672-3.18990.29131680.27082997X-RAY DIFFRACTION92
3.1899-3.3350.35051860.26023256X-RAY DIFFRACTION99
3.335-3.51080.3331630.23633279X-RAY DIFFRACTION100
3.5108-3.73060.31351770.24033270X-RAY DIFFRACTION99
3.7306-4.01840.23931910.21893269X-RAY DIFFRACTION100
4.0184-4.42230.26041820.21553319X-RAY DIFFRACTION100
4.4223-5.06120.2511650.20023348X-RAY DIFFRACTION100
5.0612-6.37250.30151720.23693374X-RAY DIFFRACTION100
6.3725-40.36910.28611660.24043471X-RAY DIFFRACTION98

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