[English] 日本語
Yorodumi
- PDB-4r4g: Crystal structure of a putative lipoprotein (ycdA) from Bacillus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r4g
TitleCrystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution
Componentsputative lipoprotein YcdA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / N-terminal domain has Ig-like fold / belongs to DUF4352 family (PF11611) / C-terminal domain has fold: alpha(2)-beta(2)-alpha(2)-beta-alpha / domains connected by kinked-helix / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF5105 / Domain of unknown function (DUF5105) / Domain of unknown function DUF4352 / Domain of unknown function (DUF4352) / Immunoprotective extracellular, immunoglobulin-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane raft / plasma membrane / Uncharacterized lipoprotein YcdA
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.62 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 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 1.4Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: putative lipoprotein YcdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8694
Polymers36,2871
Non-polymers5833
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.653, 98.653, 195.018
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein putative lipoprotein YcdA


Mass: 36286.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: ycdA, BSU02780 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: O34538
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50.0% polyethylene glycol 200, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97971,0.91837,0.97926
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979711
20.918371
30.979261
ReflectionResolution: 2.62→49.327 Å / Num. obs: 17632 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 84.781 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.88
Reflection shell

Rmerge(I) obs: 0.023 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.62-2.710.9061.821199164016382.39699.9
2.71-2.820.8882.520805175317451.52699.5
2.82-2.950.959423416174917440.92699.7
2.95-3.10.9856.422234166716670.553100
3.1-3.30.99210.223782179517940.3199.9
3.3-3.550.99716.821857170917060.17199.8
3.55-3.910.99925.521926177117690.09599.9
3.91-4.470.99939.423315177217720.062100
4.47-5.61148.621313179317900.04799.8
5.61164.823313200719920.03199.3

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.62→49.327 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9075 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG (PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 889 5.06 %RANDOM
Rwork0.2135 ---
obs0.2147 17574 99.87 %-
Displacement parametersBiso max: 166.83 Å2 / Biso mean: 89.4081 Å2 / Biso min: 49.68 Å2
Baniso -1Baniso -2Baniso -3
1--13.4645 Å20 Å20 Å2
2---13.4645 Å20 Å2
3---26.9289 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å
Refinement stepCycle: LAST / Resolution: 2.62→49.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 39 33 2557
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1282SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2586HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion346SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2830SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2586HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3479HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion3.12
LS refinement shellResolution: 2.62→2.78 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2875 156 5.66 %
Rwork0.2574 2600 -
all0.2591 2756 -
obs--99.87 %
Refinement TLS params.Method: refined / Origin x: 1.5638 Å / Origin y: 39.7534 Å / Origin z: 86.9264 Å
111213212223313233
T-0.1615 Å20.0897 Å2-0.1061 Å2-0.0414 Å2-0.016 Å2---0.1197 Å2
L0.6088 °2-0.0593 °22.0175 °2-0.5434 °20.7999 °2--8.3155 °2
S-0.2117 Å °-0.0877 Å °0.0287 Å °0.1853 Å °0.1074 Å °0.0081 Å °-0.4138 Å °-0.3718 Å °0.1043 Å °
Refinement TLS groupSelection details: {A|33 - 354}

+
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