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- PDB-7f0e: Crystal Structure of EnPKS2 -

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Basic information

Entry
Database: PDB / ID: 7f0e
TitleCrystal Structure of EnPKS2
ComponentsEnPKS2
KeywordsTRANSFERASE / k10
Function / homologyThiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesErythroxylum novogranatense (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsHuang, S.X. / Yan, Y.J.
CitationJournal: To Be Published
Title: Crystal Structure of EnPKS2
Authors: Huang, S.X. / Yan, Y.J.
History
DepositionJun 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / struct / struct_keywords
Item: _citation.title / _entity.pdbx_description ..._citation.title / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct.title / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EnPKS2
B: EnPKS2
C: EnPKS2
D: EnPKS2


Theoretical massNumber of molelcules
Total (without water)171,0704
Polymers171,0704
Non-polymers00
Water1,11762
1
A: EnPKS2


Theoretical massNumber of molelcules
Total (without water)42,7681
Polymers42,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: EnPKS2


Theoretical massNumber of molelcules
Total (without water)42,7681
Polymers42,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: EnPKS2


Theoretical massNumber of molelcules
Total (without water)42,7681
Polymers42,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: EnPKS2


Theoretical massNumber of molelcules
Total (without water)42,7681
Polymers42,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.180, 112.950, 154.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
EnPKS2


Mass: 42767.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythroxylum novogranatense (plant) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Lithium nitrate, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.62→91.22 Å / Num. obs: 51197 / % possible obs: 99.7 % / Redundancy: 13.1 % / Biso Wilson estimate: 54.45 Å2 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.052 / Net I/σ(I): 11.5
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3074 / CC1/2: 0.9 / Rpim(I) all: 0.421 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJY

4yjy


Resolution: 2.62→91.22 Å / SU ML: 0.3725 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1999 3.95 %
Rwork0.196 48654 -
obs0.1981 50653 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.11 Å2
Refinement stepCycle: LAST / Resolution: 2.62→91.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11536 0 0 62 11598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010211759
X-RAY DIFFRACTIONf_angle_d1.517215935
X-RAY DIFFRACTIONf_chiral_restr0.07711860
X-RAY DIFFRACTIONf_plane_restr0.00922033
X-RAY DIFFRACTIONf_dihedral_angle_d13.96891602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.690.35141410.28633432X-RAY DIFFRACTION99.58
2.69-2.760.36121400.27413406X-RAY DIFFRACTION99.22
2.76-2.840.32861410.25763441X-RAY DIFFRACTION99.56
2.84-2.930.32891400.25843411X-RAY DIFFRACTION99.52
2.93-3.040.29341420.25283433X-RAY DIFFRACTION99.72
3.04-3.160.35861400.23853443X-RAY DIFFRACTION99.64
3.16-3.30.29521420.22483467X-RAY DIFFRACTION99.7
3.3-3.480.27361410.2213430X-RAY DIFFRACTION99.8
3.48-3.690.27941440.2093492X-RAY DIFFRACTION99.73
3.69-3.980.24651430.18923478X-RAY DIFFRACTION99.83
3.98-4.380.24071430.16993483X-RAY DIFFRACTION99.89
4.38-5.010.19331440.15233521X-RAY DIFFRACTION99.97
5.01-6.310.23831470.18553558X-RAY DIFFRACTION99.95
6.31-91.220.17421510.16083659X-RAY DIFFRACTION98.6

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