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- PDB-5h9g: apo-ACP from Helicobacter pylori -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5h9g
Titleapo-ACP from Helicobacter pylori
ComponentsAcyl carrier protein
KeywordsLIPID TRANSPORT / ACP / fatty acid biosynthesis / Helicobacter pylori
Function / homology
Function and homology information


acyl carrier activity / phosphopantetheine binding / cytoplasm
Similarity search - Function
Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori P12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhang, L. / Zhang, L. / Shen, X. / Jiang, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21210003 China
National Natural Science Foundation of China21572133 China
National Natural Science Foundation of China91413102 China
CitationJournal: To Be Published
Title: apo-ACP from Helicobacter pylori
Authors: Zhang, L. / Zhang, L. / Shen, X. / Jiang, H.
History
DepositionDec 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Acyl carrier protein
B: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)19,2762
Polymers19,2762
Non-polymers00
Water73941
1
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,6381
Polymers9,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)9,6381
Polymers9,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.596, 49.596, 72.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Acyl carrier protein / / ACP


Mass: 9637.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori P12 (bacteria) / Strain: P12 / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: B6JLE2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 4.5
Details: 0.1 M sodium acetate trihydrate, 3.0 M Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6091 / % possible obs: 100 % / Redundancy: 2.4 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.4 / % possible all: 98.3

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T8K

1t8k


Resolution: 2.6→15 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2855 315 5.1 %
Rwork0.2405 5776 -
obs-6091 99.4 %
Solvent computationBsol: 37.6428 Å2
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 36.8326 Å2 / Biso min: 7.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.802 Å2-8.472 Å20 Å2
2---4.376 Å20 Å2
3---10.178 Å2
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 0 41 1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1161.5
X-RAY DIFFRACTIONc_scbond_it1.7772
X-RAY DIFFRACTIONc_mcangle_it1.882
X-RAY DIFFRACTIONc_scangle_it2.7342.5
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.3487 32 5.4 %
Rwork0.2407 564 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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