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- PDB-7vyu: Crystal structure of NatS -

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Basic information

Entry
Database: PDB / ID: 7vyu
TitleCrystal structure of NatS
Components3-oxoacyl-ACP synthase
KeywordsTRANSFERASE / 3-ketoacyl-ACP synthase III homologues
Function / homology3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Thiolase-like / fatty acid biosynthetic process / cytoplasm / 3-oxoacyl-ACP synthase
Function and homology information
Biological speciesStreptomyces sp. Tu 6176 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsYu, Y. / He, C. / Wu, L. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570033 China
CitationJournal: To Be Published
Title: Crystal structure of NatS
Authors: Yu, Y. / He, C. / Wu, L. / Zhang, Y.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-ACP synthase
B: 3-oxoacyl-ACP synthase


Theoretical massNumber of molelcules
Total (without water)75,5132
Polymers75,5132
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-38 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.830, 102.830, 66.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 5 - 342 / Label seq-ID: 11 - 348

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein 3-oxoacyl-ACP synthase / 3-oxoacyl-ACP synthase III


Mass: 37756.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. Tu 6176 (bacteria) / Gene: natS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A022MLV4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, magnesium sulphate, glycerol, Tris(hydroxymethyl)methyl aminomethane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→37.03 Å / Num. obs: 72375 / % possible obs: 99.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 28.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.043 / Rrim(I) all: 0.14 / Net I/σ(I): 11.2 / Num. measured all: 737467 / Scaling rejects: 118
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.849.61.0983743339190.6590.3661.1591.991.8
9.01-37.0310.70.07862075810.9970.0240.08227.198.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHENIX1.19.2-4158model building
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→33.66 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 3616 5 %
Rwork0.181 68697 -
obs0.1822 72313 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.13 Å2 / Biso mean: 32.4664 Å2 / Biso min: 14.52 Å2
Refinement stepCycle: final / Resolution: 1.8→33.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 0 288 5334
Biso mean---36.14 -
Num. residues----676
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2062X-RAY DIFFRACTION1.033TORSIONAL
12B2062X-RAY DIFFRACTION1.033TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.830.40471230.37822331245489
1.83-1.850.31681390.316626542793100
1.85-1.880.31631400.280526512791100
1.88-1.910.32421410.267226772818100
1.91-1.940.30881390.255626442783100
1.94-1.970.24141400.212726652805100
1.97-20.23151410.199526682809100
2-2.040.20781370.195326182755100
2.04-2.080.24491420.2042682282499
2.08-2.120.21741380.197426352773100
2.12-2.170.21761400.19726472787100
2.17-2.220.21071400.198726602800100
2.22-2.270.22081400.180526722812100
2.27-2.330.17951390.178626332772100
2.33-2.40.1981410.181526872828100
2.4-2.480.24421380.18526202758100
2.48-2.570.22611420.189226892831100
2.57-2.670.24911390.186826452784100
2.67-2.790.22641390.186126472786100
2.79-2.940.20521400.18526512791100
2.94-3.120.21981400.181426692809100
3.12-3.360.20991400.173426472787100
3.36-3.70.18221390.169726442783100
3.7-4.230.18881400.154926672807100
4.24-5.340.1551400.150926532793100
5.34-33.660.15671390.16172641278099

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