[English] 日本語
Yorodumi
- PDB-1u9c: Crystallographic structure of APC35852 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u9c
TitleCrystallographic structure of APC35852
ComponentsAPC35852
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / MCSG / Parkinson's disease / chaperone / cysteine protease / PSI / Midwest Center for Structural Genomics
Function / homologyDJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Hypothetical conserved protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBorek, D. / Chen, Y. / Shao, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structural analysis of DJI superfamily
Authors: Borek, D. / Chen, Y. / Shao, D. / Collart, F. / Joachimiak, A. / Otwinowski, Z.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 19, 2014Group: Non-polymer description
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: APC35852


Theoretical massNumber of molelcules
Total (without water)24,7411
Polymers24,7411
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.183, 66.183, 53.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein APC35852


Mass: 24740.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5KWF3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.2M magnesium sulfate heptahydrate, 20% w/v PEG 3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9797 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Apr 12, 2004
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SAGITALLY FOCUSED SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 47601 / Num. obs: 49550 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.236 / Net I/σ(I): 53.7
Reflection shellResolution: 1.35→1.4 Å / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3715 / % possible all: 72.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RW7

1rw7
PDB Unreleased entry


Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.791 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.053 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19729 2484 5 %RANDOM
Rwork0.17215 ---
all0.1734 49550 --
obs0.1734 46862 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 0 187 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211763
X-RAY DIFFRACTIONr_bond_other_d0.0010.021574
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9392392
X-RAY DIFFRACTIONr_angle_other_deg0.89633668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25624.40584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391511
X-RAY DIFFRACTIONr_chiral_restr0.2910.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021982
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
X-RAY DIFFRACTIONr_nbd_refined0.2370.2356
X-RAY DIFFRACTIONr_nbd_other0.1810.21601
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2886
X-RAY DIFFRACTIONr_nbtor_other0.0860.21041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.218
X-RAY DIFFRACTIONr_symmetry_hbond_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.4671.51386
X-RAY DIFFRACTIONr_mcbond_other0.3741.5453
X-RAY DIFFRACTIONr_mcangle_it1.75321771
X-RAY DIFFRACTIONr_scbond_it2.8393758
X-RAY DIFFRACTIONr_scangle_it3.794.5621
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 125 -
Rwork0.232 2573 -
obs-3715 71.93 %
Refinement TLS params.Method: refined / Origin x: 25.224 Å / Origin y: 10.158 Å / Origin z: 40.107 Å
111213212223313233
T-0.0615 Å2-0.0004 Å20.0238 Å2--0.0196 Å20.0231 Å2---0.0439 Å2
L2.7258 °2-0.801 °2-0.6458 °2-1.0132 °20.2941 °2--1.1619 °2
S0.1255 Å °0.0243 Å °0.3659 Å °-0.0364 Å °0.0469 Å °-0.1367 Å °-0.113 Å °-0.0538 Å °-0.1724 Å °

+
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://pdbjlvh1.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