[English] 日本語
Yorodumi
- PDB-4lu1: Crystal structure of the uncharacterized Maf protein YceF from E.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lu1
TitleCrystal structure of the uncharacterized Maf protein YceF from E. coli, mutant D69A
ComponentsMaf-like protein YceF
KeywordsHYDROLASE / Maf protein / putative pyrophosphatase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homologyMaf protein - #10 / Maf protein / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsDong, A. / Xu, X. / Cui, H. / Tchigvintsev, A. / Flick, R. / Brown, G. / Popovic, A. / Yakunin, A.F. / Savchenko, A. / Structural Genomics Consortium (SGC)
CitationJournal: Chem.Biol. / Year: 2013
Title: Biochemical and structural studies of conserved maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.
Authors: Tchigvintsev, A. / Tchigvintsev, D. / Flick, R. / Popovic, A. / Dong, A. / Xu, X. / Brown, G. / Lu, W. / Wu, H. / Cui, H. / Dombrowski, L. / Joo, J.C. / Beloglazova, N. / Min, J. / ...Authors: Tchigvintsev, A. / Tchigvintsev, D. / Flick, R. / Popovic, A. / Dong, A. / Xu, X. / Brown, G. / Lu, W. / Wu, H. / Cui, H. / Dombrowski, L. / Joo, J.C. / Beloglazova, N. / Min, J. / Savchenko, A. / Caudy, A.A. / Rabinowitz, J.D. / Murzin, A.G. / Yakunin, A.F.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maf-like protein YceF
B: Maf-like protein YceF


Theoretical massNumber of molelcules
Total (without water)48,2134
Polymers48,2132
Non-polymers02
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-13 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.651, 52.834, 129.275
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Maf-like protein YceF


Mass: 24106.373 Da / Num. of mol.: 2 / Mutation: D69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: yceF / Plasmid: p15TVL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QYM5
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.79 Å3/Da / Density % sol: 31.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 20% PEG10K, 1/10 papain in protein, temperature 291K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 18, 2013 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. all: 27172 / Num. obs: 27172 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.144 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.92-1.954.50.64412940.747195.1
1.95-1.995.40.5312730.738196.1
1.99-2.0360.42313380.742198.7
2.03-2.076.80.39412870.849198.7
2.07-2.116.80.34713680.8199.4
2.11-2.1670.29713251.127199.5
2.16-2.227.10.22513840.8021100
2.22-2.287.30.21713080.9391100
2.28-2.347.40.18113520.845199.9
2.34-2.427.40.15913550.848199.9
2.42-2.517.60.13613580.8361100
2.51-2.617.70.1213640.831100
2.61-2.727.70.09813580.8871100
2.72-2.877.90.08313560.9081100
2.87-3.057.90.06513750.9851100
3.05-3.287.90.05113741.1291100
3.28-3.617.80.0513871.7371100
3.61-4.147.60.04913942.5791100
4.14-5.217.60.04114242.2331100
5.21-506.90.03414981.626198.4

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JHC

4jhc


Resolution: 1.92→33.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.961 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 856 3.2 %RANDOM
Rwork0.1994 ---
obs0.201 27031 98.75 %-
all-27172 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.44 Å2 / Biso mean: 35.0588 Å2 / Biso min: 16.03 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.92→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 2 139 2957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192894
X-RAY DIFFRACTIONr_bond_other_d0.0010.022771
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9783931
X-RAY DIFFRACTIONr_angle_other_deg0.74436362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.665375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71623.651126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54615483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0941523
X-RAY DIFFRACTIONr_chiral_restr0.0710.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_mcbond_it2.0883.3291482
X-RAY DIFFRACTIONr_mcbond_other2.0883.3281481
X-RAY DIFFRACTIONr_mcangle_it3.2884.971848
LS refinement shellResolution: 1.918→1.968 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 56 -
Rwork0.255 1780 -
all-1836 -
obs--91.94 %

+
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