[English] 日本語
Yorodumi
- PDB-3b1z: Crystal structure of an S. thermophilus NFeoB T35S mutant without... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b1z
TitleCrystal structure of an S. thermophilus NFeoB T35S mutant without nucleotide
ComponentsFerrous iron uptake transporter protein B
KeywordsMETAL TRANSPORT / G protein / iron transport / GTPase / transmembrane / potassium
Function / homology
Function and homology information


ferrous iron transmembrane transporter activity / GTP binding / metal ion binding / plasma membrane
Similarity search - Function
Helix Hairpins - #1770 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. ...Helix Hairpins - #1770 / Ferrous iron transport protein B, C-terminal / Ferrous iron transport protein B C terminus / FeoB, cytosolic helical domain / FeoB cytosolic helical domain / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain / : / Ferrous iron transport protein B / FeoB-type guanine nucleotide-binding (G) domain profile. / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition / GTP binding domain / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ferrous iron transport protein B
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAsh, M.R. / Maher, M.J. / Guss, J.M. / Jormakka, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: A suite of Switch I and Switch II mutant structures from the G-protein domain of FeoB
Authors: Ash, M.R. / Maher, M.J. / Guss, J.M. / Jormakka, M.
History
DepositionJul 15, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferrous iron uptake transporter protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2852
Polymers30,1891
Non-polymers961
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.4, 59.9, 85.3
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ferrous iron uptake transporter protein B


Mass: 30189.123 Da / Num. of mol.: 1 / Fragment: NFeoB, UNP residues 1-270 / Mutation: T35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Strain: LMG 18311 / Gene: FeoB / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5M586
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.88 Å3/Da / Density % sol: 34.53 % / Mosaicity: 0.701 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 2%(v/v) PEG 400, 2M (NH4)2SO4, pH 7.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 7047 / Num. obs: 7047 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.119 / Χ2: 1.117 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.65-2.74.90.6482.13430.87798.6
2.7-2.746.10.5293470.96599.7
2.74-2.86.90.5063370.95100
2.8-2.857.10.4883401.053100
2.85-2.927.20.3893471.114100
2.92-2.987.20.3283521.076100
2.98-3.067.30.3263341.193100
3.06-3.147.20.273481.295100
3.14-3.237.20.2183461.158100
3.23-3.347.20.2083471.287100
3.34-3.467.10.1663441.247100
3.46-3.67.10.1413491.174100
3.6-3.767.10.1173581.281100
3.76-3.967.20.1053431.136100
3.96-4.2170.0953521.061100
4.21-4.5370.0773601.068100
4.53-4.996.90.0773611.062100
4.99-5.716.90.0823611.057100
5.71-7.196.70.0783721.055100
7.19-505.80.064061.08898.8

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LX8

3lx8


Resolution: 2.65→49 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 33.854 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2841 685 9.8 %RANDOM
Rwork0.2192 ---
obs0.2258 6959 98.96 %-
all-6959 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.54 Å2 / Biso mean: 48.3688 Å2 / Biso min: 23.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å20 Å2
2--0.78 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 5 9 1921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221938
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9692641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7625249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.13725.0683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97615320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6211511
X-RAY DIFFRACTIONr_chiral_restr0.060.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211440
X-RAY DIFFRACTIONr_mcbond_it1.4973.51250
X-RAY DIFFRACTIONr_mcangle_it2.50252023
X-RAY DIFFRACTIONr_scbond_it1.3563688
X-RAY DIFFRACTIONr_scangle_it2.0344.5618
LS refinement shellResolution: 2.647→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 53 -
Rwork0.286 436 -
all-489 -
obs-489 97.02 %
Refinement TLS params.Method: refined / Origin x: 16.257 Å / Origin y: -7.728 Å / Origin z: -16.926 Å
111213212223313233
T0.1848 Å20.0208 Å20.0015 Å2-0.1626 Å20.0151 Å2--0.1934 Å2
L1.3751 °2-0.078 °20.2107 °2-0.788 °20.0588 °2--1.622 °2
S-0.0065 Å °0.0694 Å °0.1141 Å °-0.0412 Å °0.0134 Å °0.0924 Å °-0.1011 Å °-0.1229 Å °-0.0069 Å °

+
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