[English] 日本語
Yorodumi
- PDB-2oc6: Crystal structure of a protein from the duf1801 family (ydhg, bsu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oc6
TitleCrystal structure of a protein from the duf1801 family (ydhg, bsu05750) from bacillus subtilis at 1.75 A resolution
ComponentsYdhG protein
KeywordsUNKNOWN FUNCTION / Secretion chaperone-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / monoatomic ion transport / metal ion binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #200 / Domain of unknown function DUF1801 / Domain of unknown function (DU1801) / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Intracellular iron chaperone frataxin
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_388456.1) from Bacillus subtilis at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0), FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YdhG protein
B: YdhG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,22913
Polymers29,2702
Non-polymers95911
Water3,441191
1
A: YdhG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2228
Polymers14,6351
Non-polymers5867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YdhG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0085
Polymers14,6351
Non-polymers3724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.782, 46.903, 64.568
Angle α, β, γ (deg.)90.000, 110.050, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21B-135-

HOH

-
Components

#1: Protein YdhG protein


Mass: 14635.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ydhG / Production host: Escherichia coli (E. coli) / References: UniProt: Q797E6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.37 Å3/Da / Density % sol: 48.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 32.0% polyethylene glycol 8000, 0.25M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97921, 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979421
ReflectionResolution: 1.75→37.113 Å / Num. obs: 23448 / % possible obs: 85.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.078 / Χ2: 1.07 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.811.90.32211050.876140.2
1.81-1.892.30.33316180.93159
1.89-1.972.60.2820290.953174.9
1.97-2.072.90.20823061.068184.6
2.07-2.23.10.18225891.006193.8
2.2-2.383.30.15926871.1198.2
2.38-2.613.50.14127301.186199.5
2.61-2.993.60.10327701.1461100
2.99-3.773.60.07127761.0981100
3.77-503.50.05228380.998199.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
DENZOdata reduction
autoSHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→37.113 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.498 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THERE IS UNMODELED DENSITY NEAR RESIDUES B26 AND B40. 5. THE NOMINAL RESOLUTION IS 1.90 A WITH 2925 OBSERVED REFLECTIONS BETWEEN 1.90-1.75 (48.5% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 6. SULFATE, GLYCEROL, AND ACETATE WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1168 5 %RANDOM
Rwork0.173 ---
obs0.175 23443 84.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å21.91 Å2
2---0.16 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 59 191 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222175
X-RAY DIFFRACTIONr_bond_other_d0.0010.021918
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9432975
X-RAY DIFFRACTIONr_angle_other_deg0.7634446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20224.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88815333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.692158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022403
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined0.2040.2449
X-RAY DIFFRACTIONr_nbd_other0.1670.21887
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21058
X-RAY DIFFRACTIONr_nbtor_other0.0820.21151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.213
X-RAY DIFFRACTIONr_mcbond_it1.65331384
X-RAY DIFFRACTIONr_mcbond_other0.4023510
X-RAY DIFFRACTIONr_mcangle_it2.21252085
X-RAY DIFFRACTIONr_scbond_it3.881008
X-RAY DIFFRACTIONr_scangle_it4.68311880
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 37 -
Rwork0.25 662 -
obs-699 33.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6198-0.7384-1.34212.13460.36932.0419-0.109-0.1396-0.01790.04930.05530.0378-0.01260.03280.0538-0.1005-0.00380.0443-0.13410.0119-0.093217.137519.501813.5416
23.92031.1414-1.50532.3493-0.35721.8218-0.14610.13690.0163-0.09280.1-0.01020.0225-0.0360.0461-0.0855-0.00660.0477-0.1408-0.0035-0.0788-2.2996-4.045817.4014
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 123 / Label seq-ID: 1 - 124

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

+
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