[English] 日本語
Yorodumi
- PDB-3qsl: Structure of CAE31940 from Bordetella bronchiseptica RB50 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qsl
TitleStructure of CAE31940 from Bordetella bronchiseptica RB50
ComponentsPutative exported protein
KeywordsStructural genomics / Unknown function / unknown / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


alkanesulfonate transmembrane transport / periplasmic space
Similarity search - Function
NMT1-like family / Bacterial periplasmic substrate-binding proteins / Solute-binding protein family 3/N-terminal domain of MltF / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Exported protein / Putative exported protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBajor, J. / Kagan, O. / Chruszcz, M. / Savchenko, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J Struct Funct Genomics / Year: 2014
Title: The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family.
Authors: Bajor, J. / Tkaczuk, K.L. / Chruszcz, M. / Chapman, H. / Kagan, O. / Savchenko, A. / Minor, W.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative exported protein
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8874
Polymers72,5032
Non-polymers3842
Water4,017223
1
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4442
Polymers36,2511
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4442
Polymers36,2511
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.913, 65.026, 160.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 6 / Auth seq-ID: 29 - 345 / Label seq-ID: 29 - 345

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Putative exported protein


Mass: 36251.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB1442 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q7WME9, UniProt: A0A0H3LJQ6*PLUS
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.19 Å3/Da / Density % sol: 43.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M NH4Acetate, 0.1M t-Na Citrate pH5.6, 30% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 42946 / Num. obs: 42946 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 30.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1723 / Rsym value: 0.71 / % possible all: 78.6

-
Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
CCP4model building
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.198 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.187 / ESU R Free: 0.165
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23115 2168 5.1 %RANDOM
Rwork0.18834 ---
all0.19047 40683 --
obs0.19047 40683 97.44 %-
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: 48.537 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20 Å20 Å2
2--4.52 Å20 Å2
3----5.97 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 26 223 4901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224786
X-RAY DIFFRACTIONr_bond_other_d0.0010.023130
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9776512
X-RAY DIFFRACTIONr_angle_other_deg0.96737711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4925648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11325.26173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53815732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.991516
X-RAY DIFFRACTIONr_chiral_restr0.0880.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02900
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.53194
X-RAY DIFFRACTIONr_mcbond_other0.1991.51324
X-RAY DIFFRACTIONr_mcangle_it1.25725069
X-RAY DIFFRACTIONr_scbond_it2.3931592
X-RAY DIFFRACTIONr_scangle_it3.5344.51440
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3793 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.385
loose thermal3.3410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 143 -
Rwork0.323 2416 -
obs--80.75 %
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)
12.56740.2134-1.37622.0021-0.22243.4466-0.26340.2007-0.3984-0.06580.1130.09530.390.07720.15040.05860.00380.0510.0571-0.02270.130946.3318.1794.01
21.50720.1446-0.53281.44410.21873.7907-0.06530.16450.1695-0.11170.08620.1468-0.506-0.2332-0.0210.09350.0274-0.0010.05280.02610.152242.69634.0331.399
33.86320.1377-1.70362.150.08524.7491-0.0901-0.27710.17290.20130.12860.2245-0.33360.0324-0.03840.0860.05040.02160.0526-0.01660.144643.55129.53616.657
42.9778-0.38031.32351.5388-1.05025.09090.16070.1202-0.0432-0.1512-0.2866-0.07460.1450.61850.1260.0690.01620.00760.10130.03640.099959.94830.9-33.383
52.9726-0.2941.29411.0999-1.00814.74230.3249-0.075-0.4339-0.2351-0.00120.21320.8469-0.7114-0.32360.2518-0.1272-0.07050.13990.01140.252642.82823.433-39.835
62.4040.51622.61530.3307-0.451713.666-0.30250.21390.4540.0633-0.10680.0742-1.3747-0.03390.40930.44230.0182-0.05540.22950.02350.386750.30743.277-39.915
72.90850.25761.28114.1825-2.39524.92890.1523-0.2534-0.24880.0653-0.15210.07950.0577-0.3072-0.00020.0598-0.04660.03290.08720.00240.107451.01129.716-22.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 94
2X-RAY DIFFRACTION2A95 - 289
3X-RAY DIFFRACTION3A290 - 345
4X-RAY DIFFRACTION4B29 - 114
5X-RAY DIFFRACTION5B115 - 246
6X-RAY DIFFRACTION6B247 - 290
7X-RAY DIFFRACTION7B291 - 345

+
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