[English] 日本語
Yorodumi
- PDB-3gfv: Crystal Structure of Petrobactin-binding Protein YclQ from Bacill... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gfv
TitleCrystal Structure of Petrobactin-binding Protein YclQ from Bacillu subtilis
ComponentsUncharacterized ABC transporter solute-binding protein yclQ
KeywordsTRANSPORT PROTEIN / alpha-beta-sandwich / periplasmic binding protein fold (PBP fold) / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Secreted / Transport / unknown function
Function / homology
Function and homology information


: / iron ion transport / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
FatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARAGINE / PHOSPHATE ION / Petrobactin-binding protein YclQ
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKim, Y. / Maltseva, N. / Zawadzka, A.M. / Raymond, K.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore.
Authors: Zawadzka, A.M. / Kim, Y. / Maltseva, N. / Nichiporuk, R. / Fan, Y. / Joachimiak, A. / Raymond, K.N.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized ABC transporter solute-binding protein yclQ
B: Uncharacterized ABC transporter solute-binding protein yclQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6284
Polymers67,4012
Non-polymers2272
Water9,170509
1
A: Uncharacterized ABC transporter solute-binding protein yclQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7952
Polymers33,7001
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized ABC transporter solute-binding protein yclQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8322
Polymers33,7001
Non-polymers1321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.602, 35.150, 95.433
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Uncharacterized ABC transporter solute-binding protein yclQ


Mass: 33700.367 Da / Num. of mol.: 2 / Fragment: residues 21-317
Source method: isolated from a genetically manipulated source
Details: C-terminal His6-tag with TEV protease cut-site
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: subsp. subtilis str. 168 / Gene: BSU03830, yclQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: P94421
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M Phosphate-citrate pH 4.2 40 %v/v PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→41.29 Å / Num. all: 55926 / Num. obs: 55926 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 26.05 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2667 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→41.286 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2823 5.07 %random
Rwork0.164 ---
all0.165 55684 --
obs0.165 55684 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.934 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2262 Å20 Å20.0577 Å2
2--5.1325 Å20 Å2
3----5.3587 Å2
Refinement stepCycle: LAST / Resolution: 1.75→41.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 13 509 5044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.149
X-RAY DIFFRACTIONf_dihedral_angle_d17.3
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.75-1.78020.24941070.21272526263396
1.7802-1.81260.25791220.2009263799
1.8126-1.84740.23161240.19142680100
1.8474-1.88510.26041370.1892600100
1.8851-1.92610.22291380.17332627100
1.9261-1.97090.18041420.16942649100
1.9709-2.02020.1781510.15442605100
2.0202-2.07480.22221420.15952700100
2.0748-2.13590.19881370.15842602100
2.1359-2.20480.21481500.162663100
2.2048-2.28360.22141450.15842602100
2.2836-2.37510.19021540.15992662100
2.3751-2.48310.19011420.15932666100
2.4831-2.6140.19151370.15822631100
2.614-2.77780.21581470.16422670100
2.7778-2.99220.18381560.17422673100
2.9922-3.29320.2041720.17232645100
3.2932-3.76950.16111320.1541267599
3.7695-4.7480.14741450.1301266598
4.748-41.29770.18641430.1674268395
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)
11.42580.1410.87270.55020.32531.0805-0.07280.09150.0349-0.06390.028-0.00960.0025-0.03320.04150.1813-0.02460.03010.21490.00320.152978.40999.114670.0522
21.9548-0.49451.15111.2719-0.43841.7120.14730.0062-0.1443-0.1367-0.02750.12650.06960.0237-0.120.1450.00310.0130.0887-0.00060.162343.338-3.508674.4847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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