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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mhf
TitleCrystal structure of a TRAP periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Glucuronate, space group P21
ComponentsTRAP dicarboxylate transporter, 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 / 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
beta-D-glucopyranuronic acid / alpha-D-glucopyranuronic acid / Solute-binding protein Bpro_3107
Similarity search - Component
Biological speciesPolaromonas (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.46 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Zhao, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Jacobson, M.P. / 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
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1113
Polymers36,7221
Non-polymers3882
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.480, 45.960, 63.980
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 36722.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas (bacteria) / Strain: JS666 / ATCC BAA-500 / Gene: Bpro_3107 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q128M1
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-GCU / alpha-D-glucopyranuronic acid / alpha-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, alpha linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGlcpAaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
a-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.8 Å3/Da / Density % sol: 31.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (> 50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Glucuronate, 5 mM DTT); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Tris, pH 8.5(MCSG1 F10)); Cryoprotection (20% Diethylene Glycol, 80% of ...Details: Protein (> 50 mg/ml, 10 mM Hepes, pH 7.5, 10 mM Glucuronate, 5 mM DTT); Reservoir (2.0 M Ammonium Sulfate, 0.1 M Tris, pH 8.5(MCSG1 F10)); Cryoprotection (20% Diethylene Glycol, 80% of Reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 23, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.46→63.409 Å / Num. all: 41662 / Num. obs: 41662 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 8.31 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.46-1.546.30.1334.93616857180.13387.8
1.54-1.646.30.1026.23469955200.10289
1.64-1.756.30.0767.83343252780.07690.7
1.75-1.896.30.05910.33156149720.05991.9
1.89-2.076.40.04712.82966946690.04793.4
2.07-2.326.40.04413.32724042890.04494.7
2.32-2.676.30.04213.82425338350.04296
2.67-3.286.30.03515.92081233090.03597.3
3.28-4.636.20.039151625726090.03998.4
4.63-22.985.90.03914.5869414630.03998.5

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.46→21.582 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9374 / SU ML: 0.09 / σ(F): 0 / σ(I): 0 / Phase error: 12.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1447 2108 5.06 %RANDOM
Rwork0.1173 ---
obs0.1187 41631 92.18 %-
all-41631 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.73 Å2 / Biso mean: 12.2561 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.46→21.582 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 0 26 471 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082416
X-RAY DIFFRACTIONf_angle_d1.2493266
X-RAY DIFFRACTIONf_chiral_restr0.074371
X-RAY DIFFRACTIONf_plane_restr0.008419
X-RAY DIFFRACTIONf_dihedral_angle_d12.029920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.49910.16041280.13832440256887
1.4991-1.53650.18291170.12432514263188
1.5365-1.57810.1431370.11542539267688
1.5781-1.62450.14431380.11312494263289
1.6245-1.67690.14181260.11492558268490
1.6769-1.73680.16311490.11522543269291
1.7368-1.80630.14931390.11612607274691
1.8063-1.88850.14981460.11362625277192
1.8885-1.9880.13831450.11212620276593
1.988-2.11240.14511560.10612648280493
2.1124-2.27540.13251390.10522716285594
2.2754-2.50410.13881390.10862728286795
2.5041-2.86570.14381550.11672765292096
2.8657-3.60770.14981640.12142794295897
3.6077-21.58390.13551300.13362932306298
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)
10.2712-0.0288-0.15480.172-0.09060.15780.00440.01490.0167-0.0313-0.03560.05420.011-0.077-0.00080.0413-0.01150.00440.0572-0.00740.04416.688519.954246.0672
20.2227-0.05680.19940.14780.06060.24310.031-0.0177-0.05960.014-0.016-0.02560.0263-0.00380.00060.0342-0.00740.00090.03530.00630.043822.939716.355649.5991
30.0966-0.0256-0.00840.18-0.19010.2063-0.03430.00450.05620.081-0.0277-0.0419-0.11420.0332-0.00310.0601-0.011-0.01060.0345-0.00230.03827.001735.363154.3022
40.04520.03330.04280.0491-0.0390.1160.02580.0791-0.01660.0114-0.08890.0094-0.07510.0551-0.00240.0579-0.0043-0.00110.03370.00650.049826.882634.865745.7745
50.2768-0.03730.09220.06330.07990.2222-0.02740.0084-0.0463-0.0679-0.01240.00170.0563-0.0208-0.00720.0429-0.01480.00420.0283-0.00540.034914.070616.465242.2632
60.0415-0.00330.06020.04410.02010.0485-0.02940.14440.1484-0.0913-0.1358-0.18450.00370.1758-0.07020.0654-0.00540.01310.10580.03590.129438.152233.304645.307
70.09460.03790.0490.02060.04120.11170.08120.0468-0.08110.06310.0288-0.06330.1260.05290.00090.0658-0.002-0.02030.06810.00450.093936.022312.775753.9085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 31:86 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 87:158 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 159:221 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 222:240 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 241:289 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 290:305 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 306:331 )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