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- PDB-7ax5: Anammox-specific acyl carrier protein from Kuenenia stuttgartiens... -

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Basic information

Entry
Database: PDB / ID: 7ax5
TitleAnammox-specific acyl carrier protein from Kuenenia stuttgartiensis; ensemble refinement
ComponentsSimilar to acyl carrier protein
KeywordsLIPID BINDING PROTEIN / anammox / ladderane / acyl carrier protein / ensemble refinement
Function / homologyPhosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / metal ion binding / Putative acyl carrier protein
Function and homology information
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.756 Å
AuthorsDietl, A. / Barends, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)724362European Union
CitationJournal: Proteins / Year: 2022
Title: Dynamics in an unusual acyl carrier protein from a ladderane lipid-synthesizing organism.
Authors: Dietl, A. / Barends, T.R.M.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Similar to acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1908
Polymers10,7321
Non-polymers4587
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-114 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.810, 76.810, 30.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Number of models75

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Components

#1: Protein Similar to acyl carrier protein


Mass: 10732.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kuenenia stuttgartiensis (bacteria) / Gene: acpP, acpP_2, KSMBR1_3472, kuste3603 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1Q2X6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% (v/v) PEG 400, 200 mM calcium acetate, 100 mM sodium acetate pH 4.5 and 10 mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.756→38.404 Å / Num. obs: 7492 / % possible obs: 91.6 % / Redundancy: 5.3 % / Rpim(I) all: 0.025 / Net I/σ(I): 16.4
Reflection shellResolution: 1.76→1.9 Å / Num. unique obs: 1132 / Rpim(I) all: 0.652

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Processing

Software
NameVersionClassification
PHENIX(phenix.ensemble_refinement:1.15.2_3472)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.756→38.404 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 369 4.95 %
Rwork0.1747 7087 -
obs0.1776 7456 70.18 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso min: 99999 Å2
Refinement stepCycle: final / Resolution: 1.756→38.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 0 0 701
Num. residues----0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.756-2.00960.309550.2234109133
2.0096-2.53190.24711340.1735258777
2.5319-38.4040.22771800.17283409100

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