[English] 日本語
Yorodumi
- PDB-4n8y: Crystal structure of a trap periplasmic solute binding protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n8y
TitleCrystal structure of a trap periplasmic solute binding protein from bradyrhizobium sp. btai1 b (bbta_0128), target EFI-510056 (bbta_0128), complex with alpha/beta-d-galacturonate
ComponentsPutative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP 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
alpha-D-galactopyranuronic acid / beta-D-galactopyranuronic acid / Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
Similarity search - Component
Biological speciesBradyrhizobium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / 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
DepositionOct 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
B: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8196
Polymers72,0432
Non-polymers7774
Water16,358908
1
A: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4103
Polymers36,0211
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4103
Polymers36,0211
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.798, 85.705, 86.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative TRAP-type C4-dicarboxylate transport system, binding periplasmic protein (DctP subunit)


Mass: 36021.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium sp. (bacteria) / Strain: BTAi1 / Gene: BBta_0128 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5E8D2
#2: Sugar ChemComp-ADA / alpha-D-galactopyranuronic acid / alpha-D-galacturonic acid / D-galacturonic acid / galacturonic acid / ALPHA D-GALACTURONIC ACID


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#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: isolated from a genetically manipulated source
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.: 908 / 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: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (56.1 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (0.1 M HEPES, 25 %(w/v) PEG 3350); Cryoprotection (20% Reservoir, 80% PEG3350 (50% w/v)), pH 7.5, VAPOR ...Details: Protein (56.1 mg/ml, 10 mM HEPES, 5 mM DTT, 10 mM D-Galacturonate); Reservoir (0.1 M HEPES, 25 %(w/v) PEG 3350); Cryoprotection (20% Reservoir, 80% PEG3350 (50% w/v)), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.971 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 9, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.971 Å / Relative weight: 1
ReflectionResolution: 1.5→86.246 Å / Num. all: 90134 / Num. obs: 90134 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.587.30.5231.593789127930.52394.4
1.58-1.687.50.3632.291527121840.36395
1.68-1.797.60.2483.188116115690.24895.5
1.79-1.947.60.1574.982347107680.15796.1
1.94-2.127.60.0977.776238100330.09796.5
2.12-2.377.60.06611.26923091440.06697
2.37-2.747.50.04715.36140181410.04797.5
2.74-3.357.50.03121.65208769540.03198
3.35-4.747.30.02228.14022254840.02298.3
4.74-85.7056.90.0229.92117330640.0295.8

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4N17

4n17


Resolution: 1.5→29.087 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9015 / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 4506 5.01 %RANDOM
Rwork0.1436 ---
obs0.1452 90027 95.8 %-
all-90027 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.83 Å2 / Biso mean: 22.6948 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 0 52 908 5592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094809
X-RAY DIFFRACTIONf_angle_d1.2156521
X-RAY DIFFRACTIONf_chiral_restr0.05738
X-RAY DIFFRACTIONf_plane_restr0.007840
X-RAY DIFFRACTIONf_dihedral_angle_d13.3751813
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 (%)
1.5-1.51710.26891370.21972796293394
1.5171-1.53490.23251660.20162723288994
1.5349-1.55360.21081410.20072779292094
1.5536-1.57330.23171500.18432773292394
1.5733-1.5940.22241570.17992763292094
1.594-1.61580.18451450.17492776292195
1.6158-1.63890.1861400.17982807294795
1.6389-1.66340.21661390.16962782292194
1.6634-1.68930.21161390.16592805294495
1.6893-1.7170.19221400.16842825296595
1.717-1.74660.20021450.16352818296395
1.7466-1.77840.19371510.15822774292595
1.7784-1.81260.20811510.15592838298996
1.8126-1.84960.18761570.14852800295796
1.8496-1.88980.18611560.1512823297996
1.8898-1.93380.18521490.15112855300496
1.9338-1.98210.17971350.15262855299096
1.9821-2.03570.19771410.14912852299396
2.0357-2.09560.18771580.15032865302396
2.0956-2.16320.16531420.1432881302396
2.1632-2.24050.17211500.14132865301597
2.2405-2.33010.18051670.13362877304497
2.3301-2.43610.15421380.13452897303597
2.4361-2.56450.16241490.12972892304197
2.5645-2.72510.15171720.13392909308197
2.7251-2.93530.16051600.1342909306997
2.9353-3.23030.1621510.13322956310798
3.2303-3.6970.15831520.13252987313998
3.697-4.65470.16821600.11572996315698
4.6547-29.09240.15741680.14543043321195
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)
10.93660.6204-0.82851.0165-0.62451.02730.0277-0.01330.0561-0.0337-0.0929-0.1341-0.05890.090.07290.1098-0.00120.01560.12050.00730.114723.05625.674-15.8358
20.50040.15980.10941.1684-0.01580.36980.0280.0468-0.0299-0.2259-0.04830.18660.0234-0.07870.01550.15370.0151-0.02480.1367-0.02770.13317.69218.1237-18.0287
30.6834-0.13480.11891.5880.07220.6461-0.0069-0.0028-0.1426-0.0887-0.01950.30140.0371-0.09610.02050.0854-0.00040.01210.1032-0.02510.16567.47147.9117-12.1126
40.45930.04940.01851.3941-0.37860.585-0.02410.0508-0.0398-0.2019-0.0628-0.07550.01160.05650.07260.13010.00690.02960.109-0.01210.090318.446814.4917-18.1674
51.2884-0.0180.74141.08040.21551.31950.08470.2431-0.3455-0.152-0.00530.36780.1742-0.0232-0.0920.1572-0.0156-0.02840.1947-0.06460.28223.7707-3.5235-16.4148
65.4906-0.8032-0.01081.2715-0.06991.6177-0.08560.14370.1242-0.38950.01150.25170.0767-0.00510.04540.4272-0.0237-0.13690.2528-0.06760.25283.87596.9591-33.7659
70.901-0.72210.98421.1133-0.60091.14130.0042-0.0184-0.0751-0.0131-0.1106-0.22580.14850.14950.10370.11940.03470.03750.15120.06020.168722.175517.396413.3136
80.4161-0.2664-0.27351.25180.23320.7431-0.05-0.0502-0.06190.0186-0.03550.05170.0691-0.00760.08310.08030.00610.01810.11960.02170.09736.631124.842914.8243
90.57150.0752-0.17650.9301-0.07490.7839-0.0285-0.0372-0.0191-0.0192-0.06030.0725-0.0389-0.01970.08510.07290.0154-0.0070.0973-0.00210.08937.444833.31710.0897
100.2788-0.15760.15431.8655-1.35181.8532-0.0421-0.1015-0.04610.1675-0.141-0.2044-0.0990.2380.17960.08890.0035-0.01170.16070.05260.143822.256229.190416.2119
110.5733-0.0102-0.00331.08310.02690.44350.0796-0.11150.10430.0556-0.10620.1737-0.1726-0.0096-0.00020.14890.0027-0.00530.1456-0.02480.14852.271347.072312.4523
125.20461.30521.12332.31180.00331.84630.1789-0.45290.11310.3297-0.08180.20590.1254-0.0652-0.06280.2497-0.00210.04910.27970.00820.15221.670136.541830.1297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 61 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 109 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 219 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 220 through 281 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 307 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 308 through 322 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 61 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 109 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 246 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 247 through 281 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 282 through 306 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 307 through 322 )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