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- PDB-4m57: Crystal structure of the pentatricopeptide repeat protein PPR10 f... -

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Basic information

Entry
Database: PDB / ID: 4m57
TitleCrystal structure of the pentatricopeptide repeat protein PPR10 from maize
ComponentsChloroplast pentatricopeptide repeat protein 10
KeywordsRNA BINDING PROTEIN / pentatricopeptide repeat / superhelical / RNA
Function / homology
Function and homology information


mRNA stabilization / chloroplast stroma / mRNA processing / mRNA binding / identical protein binding
Similarity search - Function
PPR repeat / PPR repeat / PPR repeat family / Pentatricopeptide repeat domain / Pentatricopeptide (PPR) repeat profile. / Pentatricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Pentatricopeptide repeat-containing protein 10, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.86 Å
AuthorsYin, P. / Li, Q. / Yan, C. / Liu, Y. / Yan, N.
CitationJournal: Nature / Year: 2013
Title: Structural basis for the modular recognition of single-stranded RNA by PPR proteins.
Authors: Yin, P. / Li, Q. / Yan, C. / Liu, Y. / Liu, J. / Yu, F. / Wang, Z. / Long, J. / He, J. / Wang, H.W. / Wang, J. / Zhu, J.K. / Shi, Y. / Yan, N.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chloroplast pentatricopeptide repeat protein 10


Theoretical massNumber of molelcules
Total (without water)81,4461
Polymers81,4461
Non-polymers00
Water00
1
A: Chloroplast pentatricopeptide repeat protein 10

A: Chloroplast pentatricopeptide repeat protein 10


Theoretical massNumber of molelcules
Total (without water)162,8912
Polymers162,8912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7600 Å2
ΔGint-27 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.373, 176.536, 64.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Chloroplast pentatricopeptide repeat protein 10 / Pentatricopeptide repeat10


Mass: 81445.609 Da / Num. of mol.: 1 / Fragment: UNP residues 61-786 / Mutation: C256S, C279S, C430S, C449S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: ppr10, ZEAMMB73_867042 / Production host: Escherichia coli (E. coli) / References: UniProt: B8Y6I0
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M sodium formate, 0.1M Bis-Tris propane, 0.04M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Oct 5, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.85→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.86→37.08 Å / SU ML: 0.28 / σ(F): 1.37 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 1765 5.09 %
Rwork0.24 --
obs0.24 34666 99.5 %
all-34847 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.65 Å2 / ksol: 0.39 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å20 Å2
2---16.6778 Å20 Å2
3---17.4678 Å2
Refinement stepCycle: LAST / Resolution: 2.86→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 0 0 5326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195423
X-RAY DIFFRACTIONf_angle_d1.3187353
X-RAY DIFFRACTIONf_dihedral_angle_d19.6051945
X-RAY DIFFRACTIONf_chiral_restr0.113841
X-RAY DIFFRACTIONf_plane_restr0.008945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8602-2.93750.3131340.34112395X-RAY DIFFRACTION94
2.9375-3.02390.30911380.32162516X-RAY DIFFRACTION100
3.0239-3.12140.34421330.31072546X-RAY DIFFRACTION100
3.1214-3.23290.29081290.29912575X-RAY DIFFRACTION100
3.2329-3.36230.32331260.29342535X-RAY DIFFRACTION100
3.3623-3.51520.30431420.27292522X-RAY DIFFRACTION100
3.5152-3.70040.221600.24122520X-RAY DIFFRACTION100
3.7004-3.9320.25771340.22592538X-RAY DIFFRACTION100
3.932-4.23510.22331260.21172565X-RAY DIFFRACTION100
4.2351-4.66060.20461520.19612535X-RAY DIFFRACTION100
4.6606-5.33330.18231310.21742552X-RAY DIFFRACTION100
5.3333-6.71290.3161350.28822542X-RAY DIFFRACTION100
6.7129-37.08320.25721250.19432560X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.7092 Å / Origin y: -2.2218 Å / Origin z: 9.2059 Å
111213212223313233
T0.467 Å2-0.0122 Å20.0242 Å2-0.5244 Å20.0238 Å2--0.5729 Å2
L-0.1205 °20.1278 °20.0243 °2-0.4762 °20.1931 °2--0.1999 °2
S0.0271 Å °0.0434 Å °0.0606 Å °0.0759 Å °-0.0483 Å °0.0161 Å °-0.0723 Å °0.0064 Å °0.0143 Å °
Refinement TLS groupSelection details: all

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