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- PDB-8dld: Crystal structure of chalcone-isomerase like protein from Physcom... -

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Basic information

Entry
Database: PDB / ID: 8dld
TitleCrystal structure of chalcone-isomerase like protein from Physcomitrella patens (PpCHIL-A)
ComponentsChalcone-flavonone isomerase family protein
KeywordsSIGNALING PROTEIN / Chalcone isomerase-fold
Function / homologyChalcone--flavonone isomerase 3-like / intramolecular lyase activity / Chalcone-flavanone isomerase / Chalcone isomerase, orthogonal bundle domain superfamily / Chalcone isomerase / Chalcone isomerase, 3-layer sandwich / Chalcone isomerase superfamily / Chalcone-flavonone isomerase family protein
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWolf Saxon, E. / Moorman, C. / Castro, A. / Ruiz, A. / Mallari, J.P. / Burke, J.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Regulatory ligand binding in plant chalcone isomerase-like (CHIL) proteins.
Authors: Wolf-Saxon, E.R. / Moorman, C.C. / Castro, A. / Ruiz-Rivera, A. / Mallari, J.P. / Burke, J.R.
History
DepositionJul 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chalcone-flavonone isomerase family protein


Theoretical massNumber of molelcules
Total (without water)23,5561
Polymers23,5561
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.550, 49.880, 76.820
Angle α, β, γ (deg.)90.000, 110.870, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

21A-358-

HOH

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Components

#1: Protein Chalcone-flavonone isomerase family protein


Mass: 23556.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_030203, PHYPADRAFT_167842 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9T3E4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4K and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→37.94 Å / Num. obs: 18703 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.73 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.049 / Net I/σ(I): 8.1
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2696 / Rpim(I) all: 0.326

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootmodel building
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4dok

4dok


Resolution: 1.85→37.3 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.4302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1863 9.99 %
Rwork0.185 16784 -
obs0.189 18647 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 0 158 1760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091677
X-RAY DIFFRACTIONf_angle_d1.09782289
X-RAY DIFFRACTIONf_chiral_restr0.0656263
X-RAY DIFFRACTIONf_plane_restr0.0075300
X-RAY DIFFRACTIONf_dihedral_angle_d19.5871619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.3471370.27841292X-RAY DIFFRACTION97.28
1.9-1.960.33821420.30761229X-RAY DIFFRACTION96.01
1.96-2.020.26471450.21561286X-RAY DIFFRACTION97.55
2.02-2.090.27581370.23141283X-RAY DIFFRACTION97.53
2.09-2.170.25511370.20541280X-RAY DIFFRACTION97.99
2.18-2.270.28681360.21921252X-RAY DIFFRACTION96.72
2.27-2.390.23231500.19611297X-RAY DIFFRACTION98.23
2.39-2.540.23291400.19631303X-RAY DIFFRACTION98.43
2.54-2.740.26361520.19781295X-RAY DIFFRACTION98.64
2.74-3.020.25361400.19861291X-RAY DIFFRACTION98.69
3.02-3.450.22671450.17521310X-RAY DIFFRACTION98.71
3.45-4.350.17081510.14821316X-RAY DIFFRACTION98.66
4.35-37.30.18391510.15891350X-RAY DIFFRACTION98.82
Refinement TLS params.Method: refined / Origin x: -4.81971199516 Å / Origin y: -2.36084071775 Å / Origin z: 19.9798947651 Å
111213212223313233
T0.173737776686 Å20.0187883328048 Å2-0.00765869337617 Å2-0.152758418433 Å20.00468305378039 Å2--0.166994977011 Å2
L2.18194518557 °20.161748061956 °2-0.949928337947 °2-1.61193801944 °2-0.188404114882 °2--2.78730960103 °2
S-0.0481687060534 Å °0.218497717959 Å °-0.0199519581089 Å °-0.191383464166 Å °-0.0242289447331 Å °-0.0824932383966 Å °0.182352823539 Å °-0.0242526899367 Å °0.0493224766287 Å °
Refinement TLS groupSelection details: all

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