[English] 日本語
Yorodumi
- PDB-5u4z: Crystal structure of citrus MAF1 in space group P 31 2 1 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more