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- PDB-5u4z: Crystal structure of citrus MAF1 in space group P 31 2 1 -

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Basic information

Entry
Database: PDB / ID: 5u4z
TitleCrystal structure of citrus MAF1 in space group P 31 2 1
ComponentsRepressor of RNA polymerase III transcription
KeywordsTRANSCRIPTION / repressor of RNA polymerase III
Function / homologyRepressor of RNA polymerase III transcription Maf1 / Repressor of RNA polymerase III transcription Maf1 superfamily / Maf1 regulator / negative regulation of transcription by RNA polymerase III / nucleus / Repressor of RNA polymerase III transcription
Function and homology information
Biological speciesCitrus sinensis (sweet orange)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsSoprano, A.S. / Giuseppe, P.O. / Nascimento, A.F.Z. / Benedetti, C.E. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)12/06736-6 Brazil
CitationJournal: To Be Published
Title: Crystal structure of citrus MAF1 in space group P 31 2 1
Authors: Soprano, A.S. / Giuseppe, P.O. / Nascimento, A.F.Z. / Benedetti, C.E. / Murakami, M.T.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Repressor of RNA polymerase III transcription
B: Repressor of RNA polymerase III transcription
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3894
Polymers62,1972
Non-polymers1922
Water181
1
A: Repressor of RNA polymerase III transcription
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2913
Polymers31,0981
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Repressor of RNA polymerase III transcription


Theoretical massNumber of molelcules
Total (without water)31,0981
Polymers31,0981
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.106, 86.106, 182.167
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Repressor of RNA polymerase III transcription


Mass: 31098.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrus sinensis (sweet orange) / Gene: MAF1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: G9I821
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.6
Details: 1 M ammonium di-hydrogen phosphate, 0.1 M Tris-sodium pH 5.6, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→47.086 Å / Num. obs: 35279 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 69.534 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.214 / Rrim(I) all: 0.225 / Χ2: 1.468 / Net I/σ(I): 10.94 / Num. measured all: 372748
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.85-3.022.6681.05199.9
3.02-3.231.3952.08199.9
3.23-3.490.6914.031100
3.49-3.820.3747.051100
3.82-4.270.20911.771100
4.27-4.920.11120.281100
4.92-6.010.11319.511100
6.01-8.430.08425.151100
8.43-47.0860.03753.04199.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1655 / FOM work R set: 0.7799 / SU B: 14.493 / SU ML: 0.258 / SU R Cruickshank DPI: 0.4087 / SU Rfree: 0.2769 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 975 5.2 %RANDOM
Rwork0.1975 ---
obs0.1994 17882 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.12 Å2 / Biso mean: 81.165 Å2 / Biso min: 50.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å21.1 Å20 Å2
2--2.2 Å2-0 Å2
3----7.14 Å2
Refinement stepCycle: final / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 10 1 2995
Biso mean--104.55 64.47 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193071
X-RAY DIFFRACTIONr_bond_other_d0.0030.022805
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9614149
X-RAY DIFFRACTIONr_angle_other_deg1.02536471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9325353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.53623.506154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.26515518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9081516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023385
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02755
X-RAY DIFFRACTIONr_mcbond_it4.4157.791427
X-RAY DIFFRACTIONr_mcbond_other4.4137.791426
X-RAY DIFFRACTIONr_mcangle_it6.77611.6871775
LS refinement shellResolution: 2.85→2.922 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 70 -
Rwork0.394 1285 -
all-1355 -
obs--100 %

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