[English] 日本語
Yorodumi
- PDB-4dqd: The crystal structure of a transporter in complex with 3-phenylpy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dqd
TitleThe crystal structure of a transporter in complex with 3-phenylpyruvic acid
ComponentsExtracellular ligand-binding receptor
KeywordsSIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural ge nomics / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


amino acid transport
Similarity search - Function
: / Leucine-binding protein domain / Periplasmic binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-HYDROXYPYRUVIC ACID / 3-PHENYLPYRUVIC ACID / Extracellular ligand-binding receptor
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsTan, K. / Mack, J.C. / Zerbs, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2013
Title: Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-Coumaric acid and related aromatic acids.
Authors: Tan, K. / Chang, C. / Cuff, M. / Osipiuk, J. / Landorf, E. / Mack, J.C. / Zerbs, S. / Joachimiak, A. / Collart, F.R.
History
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Extracellular ligand-binding receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7837
Polymers38,9421
Non-polymers8416
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.038, 62.422, 60.623
Angle α, β, γ (deg.)90.00, 113.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

DetailsExperimentally unknown. It is predicted to be monomeric.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Extracellular ligand-binding receptor


Mass: 38942.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_4630 / References: UniProt: Q2IR47

-
Non-polymers , 5 types, 346 molecules

#2: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3PY / 3-HYDROXYPYRUVIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide, 0.1M Tris:HCl, 20% (w/v) PEG MME 2000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.6→26 Å / Num. all: 56211 / Num. obs: 56211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 23
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2210 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3SG0

3sg0


Resolution: 1.601→25.97 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 15.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1623 2848 5.07 %random
Rwork0.1429 ---
all0.1439 56150 --
obs0.1439 56150 99.62 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.379 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7619 Å20 Å20.1312 Å2
2--6.1791 Å20 Å2
3----3.4172 Å2
Refinement stepCycle: LAST / Resolution: 1.601→25.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 57 340 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062867
X-RAY DIFFRACTIONf_angle_d1.0993877
X-RAY DIFFRACTIONf_dihedral_angle_d14.2891100
X-RAY DIFFRACTIONf_chiral_restr0.075431
X-RAY DIFFRACTIONf_plane_restr0.005506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6009-1.62850.24131350.21072535X-RAY DIFFRACTION96
1.6285-1.65810.21161490.18432661X-RAY DIFFRACTION100
1.6581-1.690.18721340.17522673X-RAY DIFFRACTION100
1.69-1.72440.18131520.16222616X-RAY DIFFRACTION100
1.7244-1.76190.20581540.15362671X-RAY DIFFRACTION100
1.7619-1.80290.17381470.14772626X-RAY DIFFRACTION100
1.8029-1.8480.19191090.14182717X-RAY DIFFRACTION100
1.848-1.89790.17371410.13862647X-RAY DIFFRACTION100
1.8979-1.95380.16221540.13262687X-RAY DIFFRACTION100
1.9538-2.01680.16551320.12792645X-RAY DIFFRACTION100
2.0168-2.08890.15231370.13092654X-RAY DIFFRACTION100
2.0889-2.17240.15661340.12942704X-RAY DIFFRACTION100
2.1724-2.27130.14581450.12912643X-RAY DIFFRACTION100
2.2713-2.39090.1581440.13552699X-RAY DIFFRACTION100
2.3909-2.54060.15611440.13762646X-RAY DIFFRACTION100
2.5406-2.73660.16161470.14752691X-RAY DIFFRACTION100
2.7366-3.01160.17461420.14482678X-RAY DIFFRACTION100
3.0116-3.44650.15061530.14262681X-RAY DIFFRACTION100
3.4465-4.3390.15191460.13142720X-RAY DIFFRACTION100
4.339-25.97360.1561490.15532708X-RAY DIFFRACTION99
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)
11.90630.57840.04061.08030.06860.93310.0935-0.28020.1310.1149-0.06250.0864-0.1171-0.0602-0.03860.15930.00010.00520.1581-0.02150.15376.81276.264933.6179
21.22380.4341-0.30121.0681-0.2970.71040.0399-0.1846-0.05520.1307-0.0419-0.06630.07380.0746-0.00020.15940.0088-0.01650.140.01070.144811.0924-6.199531.2579
31.48320.1147-0.11550.91360.05021.1592-0.07230.1999-0.1636-0.10570.0889-0.10170.1020.1741-0.02060.16150.00520.01810.1969-0.0350.161126.646-3.33359.3676
41.78670.00020.08260.54320.0170.8639-0.10560.33750.2848-0.11210.1051-0.009-0.15470.0269-0.00480.1879-0.0305-0.01080.18270.03120.160516.81197.67157.465
50.91810.4064-0.0830.8339-0.14081.1990.0089-0.02340.02390.00620.03960.13950.0485-0.1811-0.04850.13180.0085-0.00160.1443-00.1652-0.8442-2.910924.4469
63.0580.4289-0.25263.8241-0.50722.5975-0.17630.60220.0096-0.4290.13730.11560.2472-0.05310.02820.1985-0.0293-0.02830.2422-0.00130.13499.19050.74213.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 23:83)
2X-RAY DIFFRACTION2chain 'A' and (resseq 84:139)
3X-RAY DIFFRACTION3chain 'A' and (resseq 140:220)
4X-RAY DIFFRACTION4chain 'A' and (resseq 221:279)
5X-RAY DIFFRACTION5chain 'A' and (resseq 280:365)
6X-RAY DIFFRACTION6chain 'A' and (resseq 366:383)

+
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