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- PDB-4me2: Crystal Structure of THA8 protein from Brachypodium distachyon -

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Basic information

Entry
Database: PDB / ID: 4me2
TitleCrystal Structure of THA8 protein from Brachypodium distachyon
ComponentsUncharacterized protein
KeywordsRNA BINDING PROTEIN / Pentatricopeptide repeat protein / Helix-turn-helix repeats / Group II intron RNA binding / chloroplast
Function / homology
Function and homology information


Group II intron splicing / chloroplast organization / RNA binding / identical protein binding
Similarity search - Function
Protein THYLAKOID ASSEMBLY 8-like / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Pentacotripeptide-repeat region of PRORP domain-containing protein
Similarity search - Component
Biological speciesBrachypodium distachyon (stiff brome)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKe, J. / Chen, R.Z. / Ban, T. / Brunzelle, J.S. / Gu, X. / Melcher, K. / Xu, H.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structural basis for RNA recognition by a dimeric PPR-protein complex.
Authors: Ke, J. / Chen, R.Z. / Ban, T. / Zhou, X.E. / Gu, X. / Tan, M.H. / Chen, C. / Kang, Y. / Brunzelle, J.S. / Zhu, J.K. / Melcher, K. / Xu, H.E.
History
DepositionAug 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)27,7531
Polymers27,7531
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.649, 73.649, 61.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Uncharacterized protein


Mass: 27752.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachypodium distachyon (stiff brome) / Gene: BRADI2G00245, BRADI2G00270, THA8 / Plasmid: PET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I1HB13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 1.75 Å3/Da / Density % sol: 29.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 1500, 0.1 M HEPES, pH 7.5, 0.2 M L-Proline, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 31, 2013
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 25258 / Num. obs: 25258 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3660 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.286 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24394 1286 5.1 %RANDOM
Rwork0.21214 ---
obs0.21377 23941 99.98 %-
all-23946 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.301 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 0 179 1647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191496
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.9542030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3035193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7322.27366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13515237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3881517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211149
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 86 -
Rwork0.285 1701 -
obs-1701 100 %

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