[English] 日本語
Yorodumi
- PDB-1t16: Crystal structure of the bacterial fatty acid transporter FadL fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t16
TitleCrystal structure of the bacterial fatty acid transporter FadL from Escherichia coli
ComponentsLong-chain fatty acid transport protein
KeywordsLIPID TRANSPORT / beta-barrel
Function / homology
Function and homology information


long-chain fatty acid transporting porin activity / ligand-gated channel activity / cell outer membrane
Similarity search - Function
Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Outer membrane protein transport protein (OMPP1/FadL/TodX) / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Long-chain fatty acid transport protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
Authorsvan den Berg, B. / Black, P.N. / Clemons Jr., W.M. / Rapoport, T.A.
CitationJournal: Science / Year: 2004
Title: Crystal structure of the long-chain fatty acid transporter FadL.
Authors: van den Berg, B. / Black, P.N. / Clemons Jr., W.M. / Rapoport, T.A.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Long-chain fatty acid transport protein
B: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,75215
Polymers93,5342
Non-polymers2,21813
Water2,702150
1
A: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7237
Polymers46,7671
Non-polymers9566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Long-chain fatty acid transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0298
Polymers46,7671
Non-polymers1,2627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.380, 68.664, 106.024
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Long-chain fatty acid transport protein / Outer membrane fadL protein / Outer membrane flp protein


Mass: 46766.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FADL, TTR, B2344 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P10384
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, Copper(II)chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 8-BM10.97
SYNCHROTRONNSLS X2521.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.11
ReflectionResolution: 2.49→35.12 Å / Num. all: 46492 / Num. obs: 46492 / % possible obs: 100 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 47.7 Å2 / Limit h max: 39 / Limit h min: -39 / Limit k max: 27 / Limit k min: -39 / Limit l max: 42 / Limit l min: 0 / Observed criterion F max: 322738.25 / Observed criterion F min: 0.32

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→10 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 2033 5.1 %random
Rwork0.257 ---
all0.262 43671 --
obs0.262 40152 91.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 65.2399 Å2 / ksol: 0.3789 e/Å3
Displacement parametersBiso max: 172.71 Å2 / Biso mean: 72.17 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-7.88 Å20 Å2-6.08 Å2
2---13.11 Å20 Å2
3---5.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.49 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 133 150 6909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg26.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.4141995.20.38135940.0295446379369.6
2.72-2.860.4251984.50.36341870.035440438580.6
2.86-3.030.3962535.20.33946400.0255420489390.3
3.03-3.260.3572715.20.30149580.0225439522996.1
3.26-3.570.3232805.20.26650890.0195437536998.7
3.57-4.060.3162905.30.27151820.0195494547299.6
4.06-50.2552694.90.22551790.0165462544899.7
5-100.2542734.90.21352900.01555655563100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ldao.parldao.top
X-RAY DIFFRACTION3c8e4.parc8e4.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top

+
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