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- PDB-7auf: anammox-specific acyl carrier protein from Kuenenia stuttgartiens... -

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Basic information

Entry
Database: PDB / ID: 7auf
Titleanammox-specific acyl carrier protein from Kuenenia stuttgartiensis; normal refinement
ComponentsSimilar to acyl carrier protein
KeywordsLIPID BINDING PROTEIN / acyl carrier protein / ladderanes / anammox / fatty acid biosynthesis
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: 1.76 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 3, 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
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-140 kcal/mol
Surface area5590 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
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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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.: 36 / 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 / pH: 4.5
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: 1.76→38.4 Å / Num. obs: 13924 / % possible obs: 91.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.33 Å2 / Rpim(I) all: 0.025 / Net I/σ(I): 16.4
Reflection shellResolution: 1.76→1.9 Å / Num. unique obs: 1123 / Rpim(I) all: 0.652

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→38.4 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.7904 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2862 689 4.96 %
Rwork0.2301 13208 -
obs0.2327 13897 68.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.52 Å2
Refinement stepCycle: LAST / Resolution: 1.76→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms701 0 7 36 744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124707
X-RAY DIFFRACTIONf_angle_d1.3943953
X-RAY DIFFRACTIONf_chiral_restr0.0562118
X-RAY DIFFRACTIONf_plane_restr0.0077120
X-RAY DIFFRACTIONf_dihedral_angle_d6.0755440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.890.393360.3986715X-RAY DIFFRACTION18.46
1.89-2.080.28411080.3072015X-RAY DIFFRACTION52.03
2.08-2.380.35091470.26642937X-RAY DIFFRACTION75.7
2.38-30.29451980.26093730X-RAY DIFFRACTION96.77
3-38.40.27032000.20223811X-RAY DIFFRACTION98.28
Refinement TLS params.Method: refined / Origin x: 3.25345848326 Å / Origin y: 27.6610982052 Å / Origin z: 0.822406768215 Å
111213212223313233
T0.254443042875 Å2-0.0100709120267 Å2-0.111680895445 Å2-0.225067758958 Å20.0582636276123 Å2--0.314788721675 Å2
L0.391870679738 °20.160297669634 °20.0701918728789 °2-0.37883655139 °20.0507284419447 °2--0.709421263395 °2
S0.302095429098 Å °-0.0822827851409 Å °-0.765783462731 Å °-0.0703323484211 Å °-0.110191215258 Å °0.187812315044 Å °0.00343463755457 Å °-0.0996131258078 Å °0.165871867394 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 91)

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