[English] 日本語
Yorodumi
- PDB-4pf8: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pf8
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SULFITOBACTER sp. NAS-14.1 (TARGET EFI-510299) WITH BOUND BETA-D-GALACTURONATE
ComponentsTRAP-T family transporter, DctP (Periplasmic binding) subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
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
beta-D-galactopyranuronic acid / TRAP-T family transporter, DctP (Periplasmic binding) subunit
Similarity search - Component
Biological speciesSulfitobacter sp. NAS-14.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
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
DepositionApr 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Structure summary
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Oct 7, 2015Group: Experimental preparation
Revision 1.4Oct 14, 2015Group: Non-polymer description
Revision 1.5Sep 13, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRAP-T family transporter, DctP (Periplasmic binding) subunit
B: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9056
Polymers73,4452
Non-polymers4594
Water13,799766
1
A: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9523
Polymers36,7231
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TRAP-T family transporter, DctP (Periplasmic binding) subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9523
Polymers36,7231
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.979, 58.014, 62.968
Angle α, β, γ (deg.)115.620, 104.690, 94.160
Int Tables number1
Space group name H-MP1
Detailsbiological unit is a monomer

-
Components

#1: Protein TRAP-T family transporter, DctP (Periplasmic binding) subunit


Mass: 36722.688 Da / Num. of mol.: 2 / Fragment: UNP residues 30-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfitobacter sp. NAS-14.1 (bacteria) / Gene: NAS141_03681 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3T0C3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (31.8 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (2.4 M Sodium Malonate pH 7.0); Cryoprotection (80% Reservoir + 20% Diethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2014 / 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: 1.5→53.85 Å / Num. obs: 106185 / % possible obs: 94.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.41 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.056 / Net I/σ(I): 10.9 / Num. measured all: 414615
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.5-1.5340.6982.32044951750.40693.6
8.22-53.853.30.09322.815834840.0671.2

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OVQ

4ovq


Resolution: 1.5→27.923 Å / FOM work R set: 0.9075 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 10400 5 %Random Selection
Rwork0.1473 197409 --
obs0.1482 106184 92.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.58 Å2 / Biso mean: 18.16 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.5→27.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4586 0 28 766 5380
Biso mean--7.41 32.77 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114756
X-RAY DIFFRACTIONf_angle_d1.2996447
X-RAY DIFFRACTIONf_chiral_restr0.074706
X-RAY DIFFRACTIONf_plane_restr0.008845
X-RAY DIFFRACTIONf_dihedral_angle_d12.9291757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.51710.284030.26336413681693
1.5171-1.53490.26383760.25316620699692
1.5349-1.55360.23863610.24526505686693
1.5536-1.57330.2663460.23226725707193
1.5733-1.5940.26153010.22166445674693
1.594-1.61580.20643040.20976856716093
1.6158-1.63890.21533440.20516518686293
1.6389-1.66340.2263510.19546683703494
1.6634-1.68930.20883660.1876634700094
1.6893-1.7170.19893670.186678704594
1.717-1.74660.18543240.17076771709594
1.7466-1.77840.21063230.16916623694694
1.7784-1.81260.18773300.16146778710894
1.8126-1.84960.16634050.14996707711295
1.8496-1.88980.17573530.1486631698494
1.8898-1.93370.16673740.14246684705894
1.9337-1.98210.15372880.13446644693294
1.9821-2.03570.15353720.13466710708294
2.0357-2.09560.14583740.1326671704594
2.0956-2.16320.15183580.12816705706394
2.1632-2.24040.15753930.13416703709694
2.2404-2.33010.14883520.12446590694293
2.3301-2.43610.16513490.1246574692393
2.4361-2.56450.163220.13616669699193
2.5645-2.7250.14583460.13926586693293
2.725-2.93520.15243270.13736531685892
2.9352-3.23020.16383670.14276312667989
3.2302-3.69670.15293390.12536318665790
3.6967-4.65390.11852980.1176265656388
4.6539-27.92770.15772870.16065860614782
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)
12.6126-1.024-0.32271.92110.12551.03390.0520.201-0.2882-0.2959-0.0996-0.03210.52950.19910.01830.19410.05330.02380.1195-0.00930.11299.20245.54160.3065
23.0735-0.4167-0.27982.3421-0.71741.0215-0.0993-0.2463-0.04370.25380.0467-0.0286-0.01760.04750.04080.10170.0075-0.00270.10440.02340.06164.991412.015613.0639
31.0433-1.07540.44643.0213-0.15950.5917-0.0632-0.14080.04240.25480.0117-0.1626-0.06750.030.04580.0802-0.015-0.00720.1077-0.00460.09258.530823.9148.5162
41.203-0.24120.771.5341-1.22943.0824-0.08040.10280.08120.0601-0.1455-0.4599-0.1280.41620.19370.0856-0.0277-0.02030.15860.02290.185916.523326.18293.6649
51.2982-0.28730.11080.8981-0.30831.03830.06340.0390.1142-0.0349-0.04880.0095-0.1038-0.02740.00120.0759-0.0242-0.0090.04720.00680.0613-2.942528.53212.1051
61.4439-0.05010.06712.92260.23131.3982-0.0581-0.07260.10680.11840.1123-0.142-0.11430.0125-0.04910.0952-0.0020.00220.0864-0.00750.0837-8.016427.659611.0181
70.8917-0.403-0.05581.0303-0.16010.6921-0.0140.00730.0097-0.0317-0.0033-0.06090.0260.02460.01330.0575-0.0143-0.0020.06420.00960.0417-0.467620.46493.0857
83.4108-1.21050.50491.6972-0.86071.36460.05770.25410.0711-0.1893-0.1775-0.15890.19890.2370.08910.13040.01760.02560.12990.00350.05687.55716.1596-6.718
91.9954-0.11650.24632.38590.08760.8945-0.2439-0.03370.41660.05180.1755-0.4154-0.31780.1790.08140.1652-0.01310.00310.1428-0.02840.21483.691438.28565.7692
102.3764-1.30890.05483.2618-0.34241.4575-0.0496-0.19930.04170.12950.0266-0.33370.20310.44930.02030.10280.0304-0.00930.15340.01620.09673.5219-1.233428.5532
112.4602-0.1569-0.15742.7561-0.36741.38360.02450.16520.0373-0.263-0.0606-0.04510.02480.07120.02250.10240.00780.02340.09180.00830.077-3.22393.238916.0681
122.3615-0.56010.28050.69330.21620.5049-0.00030.1663-0.0695-0.09420.00280.01280.0272-0.03570.00930.1055-0.01030.00220.08020.00730.0853-14.6791-1.247820.6255
132.9361-0.466-3.27651.14470.55585.1074-0.185-0.0706-0.41830.0661-0.09740.05420.35670.01520.24790.1407-0.02020.00380.09840.00640.1449-17.1485-9.694725.4327
140.57420.059-0.13980.53180.05050.9708-0.0449-0.080.0650.07620.05410.0696-0.0202-0.10660.00120.0729-0.01290.01350.0827-0.00370.0826-20.01549.582527.1288
153.6503-1.08250.44393.61250.04651.150.05380.0288-0.2875-0.0378-0.03720.28490.0541-0.1423-0.00890.0898-0.0095-0.01140.12110.02350.1167-23.669612.597617.9694
161.0067-0.441-0.07250.5683-0.05590.8177-0.0148-0.01670.06410.02980.0132-0.0435-0.05210.00010.0020.0718-0.0134-0.00480.0577-0.00720.0662-12.835610.857124.5665
171.8903-1.1634-0.30862.48350.32242.0988-0.1957-0.2181-0.10930.34520.10130.10620.23740.06460.08730.12940.0056-0.00540.11320.02210.0525-7.2028-0.554535.5663
182.01450.61491.15832.6381.82463.39090.1972-0.191-0.03910.1121-0.19540.14050.1163-0.5083-0.00350.10860.00160.00420.13250.02090.1139-30.04578.053924.7076
191.5242-0.18741.03951.9284-0.18616.13620.1285-0.0866-0.46990.0079-0.20220.05730.381-0.52120.03490.1755-0.0506-0.05440.1869-0.00520.2557-27.918-8.541818.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 63 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 80 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 111 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 134 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 135 through 162 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 163 through 199 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 200 through 248 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 249 through 283 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 284 through 325 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 25 through 63 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 64 through 80 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 111 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 134 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 135 through 162 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 163 through 182 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 183 through 248 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 249 through 283 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 284 through 311 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 312 through 325 )B0

+
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