[English] 日本語
Yorodumi
- PDB-4ln5: Crystal structure of a trap periplasmic solute binding protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ln5
TitleCrystal structure of a trap periplasmic solute binding protein from burkholderia ambifaria (Bamb_6123), TARGET EFI-510059, with bound glycerol and chloride ion
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsTRANSPORT PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space / carbohydrate binding
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Solute-binding protein Bamb_6123
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Sep 20, 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: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5084
Polymers38,3451
Non-polymers1633
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.098, 97.340, 58.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21A-609-

HOH

31A-630-

HOH

41A-655-

HOH

-
Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 38344.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: AMMD / Gene: Bamb_6123 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B2F6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / pH: 8.5
Details: Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 5 mM DTT), Reservoir (0.8 M Lithium Chloride, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000 (MCSG1 C9)), Cryoprotection (20% ...Details: Protein (16.23 mg/ml, 10 mM HEPES pH 7.5, 150mM NaCl, 5% glycerol, 5 mM DTT), Reservoir (0.8 M Lithium Chloride, 0.1 M Tris pH 8.5, 32%(w/v) PEG 4000 (MCSG1 C9)), Cryoprotection (20% Reservoir, 80% of 50% PEG3350), sitting drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 2, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→68.386 Å / Num. all: 16289 / Num. obs: 16289 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.216.80.6681.21601823410.668100
2.21-2.357.40.5261.51634722170.526100
2.35-2.517.40.38121542920850.38199.9
2.51-2.717.40.2932.61441919560.293100
2.71-2.977.40.1894.11327818020.189100
2.97-3.327.30.1256.11201716400.125100
3.32-3.837.20.08291043414520.082100
3.83-4.770.06610.6868012410.066100
4.7-6.646.90.06210.768299840.06299.9
6.64-58.1156.40.04912.136325710.04998.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFY

2pfy


Resolution: 2.1→48.67 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8553 / SU ML: 0.23 / σ(F): 0 / σ(I): 0 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 820 5.04 %RANDOM
Rwork0.1542 ---
all0.1574 16269 --
obs0.1574 16269 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.8 Å2 / Biso mean: 25.7937 Å2 / Biso min: 8.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 8 182 2526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072404
X-RAY DIFFRACTIONf_angle_d1.0313254
X-RAY DIFFRACTIONf_chiral_restr0.07356
X-RAY DIFFRACTIONf_plane_restr0.005426
X-RAY DIFFRACTIONf_dihedral_angle_d13.637901
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.23160.2531430.182425282671100
2.2316-2.40390.27141470.176125292676100
2.4039-2.64580.24941240.180425652689100
2.6458-3.02860.2651500.171325322682100
3.0286-3.81550.21291280.145926052733100
3.8155-48.670.16641280.13112690281899
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)
10.16450.19750.06620.23950.02990.1878-0.09120.0941-0.328-0.1524-0.012-0.11270.2914-0.152-0.02190.1919-0.04270.00630.1583-0.02660.167911.603521.40473.1897
20.19050.1032-0.03290.0573-0.02020.0083-0.09230.21240.1012-0.1340.08550.0176-0.0993-0.02420.00080.14930.066-0.00210.1317-0.00790.09915.410235.5015-3.3892
30.057-0.0502-0.00810.03240.01060.0188-0.04060.07610.0729-0.0246-0.01770.0678-0.12270.033700.13290.013-0.03510.0859-0.01250.124414.383139.75376.0626
40.1333-0.22-0.04270.4055-0.08690.3496-0.0298-0.05830.1160.0932-0.0515-0.0428-0.06810.07660.00010.13120.01-0.01570.1180.00320.131322.952239.189414.2651
50.15090.03630.0260.0774-0.07970.0969-0.01750.20260.31320.1344-0.0491-0.12860.03590.190.00080.1405-0.0204-0.0240.20790.03910.166331.671242.86813.1041
60.05050.0008-0.01510.01160.01730.0189-0.08440.1874-0.137-0.1084-0.0968-0.10470.07210.0957-0.00130.15150.02420.00630.17340.04590.141733.708833.90336.339
70.13980.0565-0.05960.1772-0.26950.3066-0.0380.0690.0857-0.0145-0.0548-0.00440.01030.0646-0.0810.07160.0161-0.02260.1756-0.00730.122921.070633.59937.6527
80.15440.0073-0.22280.49980.15420.5799-0.0949-0.11840.05070.2261-0.01580.04170.2416-0.0417-0.25830.16740.0606-0.00450.10260.04160.141417.796723.825313.4113
90.1220.0555-0.09240.0749-0.10190.1796-0.0668-0.15830.0913-0.0146-0.1908-0.1425-0.25970.259-0.02020.2792-0.0311-0.11710.27390.00370.23932.780444.864618.8069
100.02240.0307-0.03870.0414-0.05120.0665-0.0342-0.04840.04660.1741-0.07040.1626-0.0907-0.19950.04340.36820.10210.05520.0139-0.1898-0.094912.931148.240822.0256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 82 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 106 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 107 through 173 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 201 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 216 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 217 through 249 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 250 through 284 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 285 through 311 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 312 through 328 )A0

+
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