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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ovt
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM OCHROBACTERIUM ANTHROPI (Oant_3902), TARGET EFI-510153, WITH BOUND L-FUCONATE
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsSOLUTE-BINDING 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
6-deoxy-L-galactonic acid / DI(HYDROXYETHYL)ETHER / TRAP dicarboxylate transporter, DctP subunit
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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
DepositionDec 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / software / struct_keywords / struct_site
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_keywords.text / _struct_site.details
Revision 1.5Jul 1, 2020Group: Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / refine_hist
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8258
Polymers74,2532
Non-polymers5736
Water13,241735
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4835
Polymers37,1261
Non-polymers3574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3423
Polymers37,1261
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.109, 123.234, 164.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-561-

HOH

21A-579-

HOH

31A-584-

HOH

-
Components

#1: Protein TRAP dicarboxylate transporter, DctP subunit


Mass: 37126.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (bacteria) / Strain: ATCC 49188 / Gene: Oant_3902 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6X5V3
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-LFC / 6-deoxy-L-galactonic acid


Type: L-saccharide / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.83 Å3/Da / Density % sol: 56.59 % / Mosaicity: 0.94 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Protein (57.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-Fuconate); Reservoir (0.2 M Sodium Chloride, 0.1 M Acetate pH 4.5, 1.26 M Ammonium Sulfate); Cryoprotection (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: Nov 20, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→98.594 Å / Num. all: 77268 / Num. obs: 77268 / % possible obs: 98.9 % / Redundancy: 14.7 % / Biso Wilson estimate: 14.15 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.181 / Rsym value: 0.16 / Net I/av σ(I): 4.037 / Net I/σ(I): 13.4 / Num. measured all: 1132887
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.914.30.8440.7880.9159020111020.220.8440.7883.898.2
1.9-2.0114.50.5580.5191.3152639105330.1450.5580.5195.798.5
2.01-2.1514.70.4080.3781.914565499050.1060.4080.3787.598.7
2.15-2.3214.80.3010.2762.113777092970.0780.3010.2769.898.9
2.32-2.5514.90.2250.2023.712772085680.0580.2250.20211.899.2
2.55-2.8514.90.1790.1594.611614978040.0460.1790.1591599.3
2.85-3.2914.90.1420.1255.310284169230.0360.1420.1252099.5
3.29-4.0214.80.1060.0926.78705658940.0270.1060.09228.299.7
4.02-5.6914.60.0730.05610.96765246210.0190.0730.05634.399.8
5.69-29.21613.90.0720.04314.63638626210.0190.0720.0433398.9

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→29.216 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8933 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1795 3903 5.05 %
Rwork0.1478 73353 -
obs0.1494 77256 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.52 Å2 / Biso mean: 18.3272 Å2 / Biso min: 3.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 34 735 5529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014932
X-RAY DIFFRACTIONf_angle_d1.1926682
X-RAY DIFFRACTIONf_chiral_restr0.074731
X-RAY DIFFRACTIONf_plane_restr0.007866
X-RAY DIFFRACTIONf_dihedral_angle_d12.9371904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8220.27231300.21482572270298
1.822-1.8450.21361260.19642596272298
1.845-1.86930.26491170.18252574269198
1.8693-1.89490.20581450.17542564270998
1.8949-1.9220.21051390.19622581272098
1.922-1.95060.19721530.16462576272998
1.9506-1.98110.19341240.15412614273898
1.9811-2.01360.20061240.14372593271798
2.0136-2.04830.16841340.14562592272698
2.0483-2.08550.22461380.15512580271898
2.0855-2.12560.18481330.13792601273499
2.1256-2.1690.18431320.13972573270599
2.169-2.21620.17631240.13652649277399
2.2162-2.26770.19291320.15292597272999
2.2677-2.32440.16921340.12912602273699
2.3244-2.38720.17171250.12962606273199
2.3872-2.45740.16211560.12512630278699
2.4574-2.53670.16931430.12842582272599
2.5367-2.62730.17971490.13242639278899
2.6273-2.73240.1771470.13252618276599
2.7324-2.85670.19751560.13922633278999
2.8567-3.00710.19641280.14742643277199
3.0071-3.19530.17231580.15362621277999
3.1953-3.44170.19321420.14692675281799
3.4417-3.78740.15651350.141926672802100
3.7874-4.33390.13761660.12672661282799
4.3339-5.45440.14851550.131527072862100
5.4544-29.22010.19831580.1932807296599
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)
10.620.17360.06580.7357-0.0450.5701-0.00040.0903-0.0241-0.17820.0075-0.05690.1723-0.034-0.01710.11110.0045-0.00180.0479-0.01340.07831.842272.334965.8917
20.32450.0128-0.01090.2454-0.00190.53610.01-0.01560.0738-0.0153-0.02970.0185-0.0941-0.30940.01940.0640.0373-0.01390.1355-0.00720.109222.723685.007877.7132
30.17640.06010.0610.1662-0.03571.08880.0324-0.01580.0632-0.0121-0.01750.03060.0768-0.168-0.02080.05190.0066-0.0050.0829-0.01090.085326.00678.798676.7255
40.82870.1442-0.86020.46380.07053.4297-0.08370.1521-0.0812-0.14730.02210.01590.2115-0.1976-0.0250.1908-0.0792-0.04650.1632-0.02240.111119.98868.525864.0327
50.4811-0.20580.2180.32710.03240.5460.07250.1159-0.0442-0.0224-0.22080.11390.0461-0.3745-0.12450.07330.073-0.01110.2987-0.04340.137314.93283.788583.7896
60.98040.00740.3150.79640.00541.27960.03480.2268-0.0267-0.1191-0.0147-0.00590.04520.1588-0.0180.11510.0243-0.00850.14140.01110.097443.679886.564629.9289
70.3937-0.15820.00610.2194-0.21210.59930.00720.06250.080.0264-0.0063-0.0154-0.1704-0.0350.00710.11250.0144-0.01110.06770.03510.099536.525997.818442.6462
80.2194-0.10680.0780.15330.00650.5569-0.01960.06220.13120.0251-0.0312-0.0492-0.25920.0770.03430.1135-0.0263-0.02070.08290.03880.115846.348696.121246.2992
90.67290.06780.82190.3488-0.14841.9770.10970.1178-0.0592-0.0136-0.050.00650.1980.165-0.09390.09610.0181-0.00390.0940.01470.119836.91581.843540.2099
100.32880.00950.05230.2897-0.33520.41270.0035-0.11160.00550.06480.00920.1107-0.2415-0.05610.01070.14490.0422-0.00850.0625-0.00060.09438.643197.646660.1103
111.94260.34510.41042.6830.08880.901-0.01290.0016-0.0060.0847-0.02080.2886-0.1438-0.1389-0.04940.22530.099-0.01620.14470.02930.239824.7315105.888547.2612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 80 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 216 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 217 through 249 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 273 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 324 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 80 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 81 through 173 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 174 through 249 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 250 through 284 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 285 through 306 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 307 through 324 )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