[English] 日本語
Yorodumi
- PDB-2prv: Crystal structure of an uncharacterized protein (yobk, bsu18990) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2prv
TitleCrystal structure of an uncharacterized protein (yobk, bsu18990) from bacillus subtilis at 1.30 A resolution
ComponentsUncharacterized protein yobK
KeywordsBIOSYNTHETIC PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


SMI1-KNR4 cell-wall / SMI1/KNR4-like / SMI1/KNR4-like / Knr4/Smi1-like domain / SMI1 / KNR4 family / Knr4/Smi1-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Immunity protein YobK
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (NP_389780.1) from Bacillus subtilis at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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
Revision 1.6Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE 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: Uncharacterized protein yobK
B: Uncharacterized protein yobK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,88619
Polymers35,7622
Non-polymers1,12317
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.128, 45.200, 48.083
Angle α, β, γ (deg.)84.540, 67.520, 73.120
Int Tables number1
Space group name H-MP1
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Uncharacterized protein yobK


Mass: 17881.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: NP_389780.1, yobK, BSU18990 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O34596
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: NANODROP, 2.5M Ammonium sulfate, 0.15M Potassium sodium tartrate, 0.1M Citric acid pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97928, 0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 6, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979281
30.978951
ReflectionResolution: 1.3→24.268 Å / Num. obs: 69476 / % possible obs: 94.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.333.90.5241.41992350450.52492.3
1.33-1.373.90.4491.71934348980.44992.6
1.37-1.413.90.38621896848030.38692.9
1.41-1.4540.3022.51836946450.30293.2
1.45-1.53.90.2433.11791145350.24393.5
1.5-1.553.90.1953.91735444010.19593.7
1.55-1.613.90.1544.91672942470.15494.2
1.61-1.683.90.1355.51631241360.13594.5
1.68-1.753.90.1056.81564039610.10594.7
1.75-1.843.90.0888.11488537730.08895.1
1.84-1.943.90.0719.51434236430.07195.5
1.94-2.063.90.05811.11360034480.05895.9
2.06-2.23.90.0512.51266032120.0596.1
2.2-2.373.90.04613.11200530540.04696.3
2.37-2.63.90.04214.71094627790.04296.8
2.6-2.913.90.04213.5994325320.04297.1
2.91-3.363.90.03914.5882522510.03997.2
3.36-4.113.90.03516.9746819100.03597.5
4.11-5.813.90.03715.8559914410.03796.4
5.81-24.393.80.04513.728977620.04592.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→24.268 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.985 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN 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 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SULFATE ION (SO4) AND ETHYLENE GLYCOL (EDO) MOLECULES FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES MSE105 AND TRP150 IN SUBUNIT A WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 3498 5 %RANDOM
Rwork0.135 ---
all0.137 ---
obs0.137 69476 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.001 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20.93 Å20.82 Å2
2---0.65 Å2-0.21 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 70 248 2801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222715
X-RAY DIFFRACTIONr_bond_other_d0.0020.021793
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9323670
X-RAY DIFFRACTIONr_angle_other_deg1.11134353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17325.66159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30915426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.872158
X-RAY DIFFRACTIONr_chiral_restr0.1890.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02577
X-RAY DIFFRACTIONr_nbd_refined0.2210.2555
X-RAY DIFFRACTIONr_nbd_other0.1920.21942
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21321
X-RAY DIFFRACTIONr_nbtor_other0.0920.21351
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.2117
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.226
X-RAY DIFFRACTIONr_mcbond_it3.22231622
X-RAY DIFFRACTIONr_mcbond_other2.1373651
X-RAY DIFFRACTIONr_mcangle_it3.99352538
X-RAY DIFFRACTIONr_scbond_it5.47281285
X-RAY DIFFRACTIONr_scangle_it7.009111129
X-RAY DIFFRACTIONr_rigid_bond_restr2.50335249
X-RAY DIFFRACTIONr_sphericity_free7.6763249
X-RAY DIFFRACTIONr_sphericity_bonded5.31634450
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 238 -
Rwork0.248 4801 -
obs-5039 92.26 %

+
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