[English] 日本語
Yorodumi
- PDB-4eyg: Crystal structure of solute binding protein of ABC transporter fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4eyg
TitleCrystal structure of solute binding protein of ABC transporter from Rhodopseudomonas palustris BisB5 in complex with vanillic acid
ComponentsTwin-arginine translocation pathway signal
KeywordsTRANSPORT PROTEIN / PSI-BIOLOGY / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS / transporter / lignin degradation product
Function / homology
Function and homology information


: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / 4-HYDROXY-3-METHOXYBENZOATE / Twin-arginine translocation pathway signal
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsChang, C. / Mack, J. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Characterization of transport proteins for aromatic compounds derived from lignin: benzoate derivative binding proteins.
Authors: Michalska, K. / Chang, C. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Twin-arginine translocation pathway signal
B: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5458
Polymers79,9662
Non-polymers5796
Water9,440524
1
A: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2724
Polymers39,9831
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Twin-arginine translocation pathway signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2724
Polymers39,9831
Non-polymers2893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.871, 130.541, 70.388
Angle α, β, γ (deg.)90.000, 109.220, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Twin-arginine translocation pathway signal


Mass: 39983.023 Da / Num. of mol.: 2 / Fragment: UNP residues 27-392
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: BisB5 / Gene: RPD_1586 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q13AR6
#2: Chemical ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M SODIUM CITRATE, 20% ISO-PROPANOL,20% PEG 4000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 66901 / Num. obs: 66219 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2789 / % possible all: 83.9

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.939 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.113
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 3349 5.1 %RANDOM
Rwork0.1349 ---
all0.1378 66140 --
obs0.1378 66140 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.32 Å2 / Biso mean: 30.4867 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å20 Å20.55 Å2
2---2.61 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.86→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5469 0 40 524 6033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025709
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.9777724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19525.294221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3911520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214290
X-RAY DIFFRACTIONr_rigid_bond_restr2.83235709
X-RAY DIFFRACTIONr_sphericity_free27.9725144
X-RAY DIFFRACTIONr_sphericity_bonded16.02955977
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 220 -
Rwork0.208 4081 -
all-4301 -
obs-4301 88.59 %
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)
10.0424-0.08380.00320.2130.02110.07-0.0125-0.0017-0.00330.05240.01250.0244-0.0018-0.002600.0330.0050.01110.00350.00350.0161-6.662534.343655.8557
20.03550.02420.00030.1148-0.01870.00380.00150.00190.003-0.0055-0.0034-0.00260.00130.00060.00190.02210.00090.00340.0018-0.00020.01542.75133.307627.8366
30.0491-0.0028-0.08870.062-0.0240.1741-0.01350.0013-0.00230.02560.01320.02010.0213-0.00730.00030.02730.00020.0070.00290.00040.0199-2.006716.155244.9511
40.0398-0.05650.07250.2564-0.08410.1344-0.0089-0.0023-0.00360.04860.014-0.0068-0.011-0.0032-0.00510.02960.00390.00440.001-0.00140.01735.416228.250258.5359
50.0053-0.01820.00330.0708-0.01250.0023-0.0032-0.002-0.00270.01450.0052-0.0001-0.0033-0.0011-0.0020.02260.00040.00150.0049-0.00120.01778.477922.505637.5809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 146
2X-RAY DIFFRACTION2A147 - 276
3X-RAY DIFFRACTION3A277 - 304
4X-RAY DIFFRACTION4A305 - 359
5X-RAY DIFFRACTION5A360 - 390

+
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