[English] 日本語
Yorodumi
- PDB-5bra: Crystal Structure of a putative Periplasmic Solute binding protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bra
TitleCrystal Structure of a putative Periplasmic Solute binding protein (IPR025997) from Ochrobactrum Anthropi ATCC49188 (Oant_2843, TARGET EFI-511085)
ComponentsPutative periplasmic binding protein with substrate ribose
KeywordsSOLUTE-BINDING PROTEIN / Periplasmic solute binding Protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / periplasmic space
Similarity search - Function
Autoinducer 2 ABC transporter, substrate-binding protein LsrB / Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Autoinducer 2-binding protein LsrB
Similarity search - Component
Biological speciesOchrobactrum anthropi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.971 Å
AuthorsYadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. ...Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be published
Title: Crystal Structure of a putative Periplasmic Solute binding protein (IPR025997) from Ochrobactrum Anthropi ATCC49188(Oant_2843, TARGET EFI-511085)
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionMay 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative periplasmic binding protein with substrate ribose


Theoretical massNumber of molelcules
Total (without water)38,5381
Polymers38,5381
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.204, 81.204, 103.629
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

-
Components

#1: Protein Putative periplasmic binding protein with substrate ribose


Mass: 38538.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168) (bacteria)
Strain: ATCC 49188 / DSM 6882 / NCTC 12168 / Gene: Oant_2843 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6X2U7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.22 Å3/Da / Density % sol: 44.51 % / Description: pyramid
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (20 mM HEPES, pH 7.5, 5 mM DTT, 10 mM D-ribulose); Reservoir (2.5M Ammonium sulphate, 0.1M TRIS, pH 8.5); Cryoprotection (80% Lithium sulfate, 20% Reservoir)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Mar 18, 2015 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.97→23.8 Å / Num. obs: 7605 / % possible obs: 100 % / Redundancy: 28.3 % / Biso Wilson estimate: 58.6 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.02 / Rrim(I) all: 0.109 / Χ2: 0.98 / Net I/av σ(I): 38.729 / Net I/σ(I): 11.3 / Num. measured all: 215050
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2
2.97-3.0229.10.9823750.9580.1840.9990.881
3.02-3.0829.20.7653660.9650.1430.7780.893
3.08-3.1328.90.6793730.9610.1270.6910.885
3.13-3.229.20.4933520.9830.0920.5020.854
3.2-3.2729.10.3853780.9810.0720.3920.878
3.27-3.34290.3113610.9910.0580.3160.892
3.34-3.4328.90.2433800.9920.0460.2470.86
3.43-3.52290.2173680.9940.0410.2210.875
3.52-3.6228.80.2173750.9920.0410.2210.963
3.62-3.7428.70.1323700.9960.0250.1351.185
3.74-3.8728.40.1093880.9970.0210.1110.816
3.87-4.03290.1013700.9970.0190.1030.851
4.03-4.2128.50.0823660.9980.0150.0830.796
4.21-4.4328.40.0763850.9970.0140.0780.839
4.43-4.7128.30.0743860.9980.0140.0750.866
4.71-5.0728.10.0863860.9990.0160.0881.229
5.07-5.5727.70.1033770.9970.020.1051.657
5.57-6.3627.30.0993990.9960.0190.1011.614
6.36-7.9626.80.0624070.9980.0120.0630.844
7.96-23.824.20.0734430.9970.0140.0740.942

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D02

3d02


Resolution: 2.971→23.615 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2951 354 4.7 %
Rwork0.179 7173 -
obs0.1843 7527 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.76 Å2 / Biso mean: 42.4013 Å2 / Biso min: 12.55 Å2
Refinement stepCycle: final / Resolution: 2.971→23.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 0 1 2372
Biso mean---21.37 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012413
X-RAY DIFFRACTIONf_angle_d1.3863274
X-RAY DIFFRACTIONf_chiral_restr0.055371
X-RAY DIFFRACTIONf_plane_restr0.005425
X-RAY DIFFRACTIONf_dihedral_angle_d15.221864
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9709-3.39970.3617940.218923522446100
3.3997-4.27910.29881260.17532334246098
4.2791-23.61560.2721340.166724872621100
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)
10.29250.1424-0.02940.29120.02070.24920.1068-0.140.2108-0.0343-0.0350.0008-0.0442-0.00440.00430.1423-0.01580.00640.2846-0.10580.2373-23.50230.3253-9.1828
20.1052-0.03820.11540.1744-0.04020.17220.0309-0.147-0.2681-0.02310.01250.12880.1456-0.1061-0.00090.2164-0.0291-0.03180.2434-0.01690.2486-16.56667.4377-12.6852
30.4213-0.18-0.22240.07940.09840.12780.0888-0.22940.4265-0.02880.08-0.3327-0.14650.1640.35780.0228-0.19120.06640.3575-0.21020.3445-13.198932.6219-4.2965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 162 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 282 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 344 )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://pdbjlvh1.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