[English] 日本語
Yorodumi
- PDB-6hce: Crystal structure of chicken riboflavin binding protein in "Apo" ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hce
TitleCrystal structure of chicken riboflavin binding protein in "Apo" form at 2.5 A resolution
ComponentsRiboflavin-binding protein
KeywordsFLAVOPROTEIN / Chicken Egg / Riboflavin / Transport
Function / homology
Function and homology information


negative regulation of sensory perception of sweet taste / negative regulation of sensory perception of bitter taste / riboflavin binding / riboflavin transport / riboflavin transmembrane transporter activity / signaling receptor activity / external side of plasma membrane
Similarity search - Function
Folate receptor / Folate receptor-like / Folate receptor family
Similarity search - Domain/homology
ACETATE ION / Riboflavin-binding protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLoch, J.I. / Lipowska, J. / Lewinski, K.
CitationJournal: To Be Published
Title: Crystal structure of chicken riboflavin binding protein in "Apo" form at 2.5 A resolution
Authors: Loch, J.I. / Lipowska, J. / Lewinski, K.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Riboflavin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,38417
Polymers27,8821
Non-polymers1,50116
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-53 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.008, 110.008, 71.629
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein / Sugars , 2 types, 3 molecules A

#1: Protein Riboflavin-binding protein / RBP


Mass: 27882.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P02752
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 6 types, 174 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.59 Å3/Da / Density % sol: 73.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3.5 M Ammonium sulfate, 100 mM HEPES; pH 7.5

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 20, 2015
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→15.44 Å / Num. obs: 17468 / % possible obs: 99.1 % / Redundancy: 3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.093 / Rrim(I) all: 0.164 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.642.60.56725460.6970.4340.71999.7
7.91-15.441.90.0314640.9980.0250.0478.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMZ

4kmz


Resolution: 2.5→14.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 11.496 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23076 1237 7.1 %RANDOM
Rwork0.18093 ---
obs0.18447 16212 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.5→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1601 0 91 160 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191758
X-RAY DIFFRACTIONr_bond_other_d0.0020.021531
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.9782376
X-RAY DIFFRACTIONr_angle_other_deg0.76833559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.322582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98215291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.01156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02388
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8141.893809
X-RAY DIFFRACTIONr_mcbond_other4.3221.877805
X-RAY DIFFRACTIONr_mcangle_it5.512.8131006
X-RAY DIFFRACTIONr_mcangle_other5.5092.8181007
X-RAY DIFFRACTIONr_scbond_it10.5662.776949
X-RAY DIFFRACTIONr_scbond_other10.5652.776949
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.6513.8311367
X-RAY DIFFRACTIONr_long_range_B_refined10.93717.1592083
X-RAY DIFFRACTIONr_long_range_B_other10.93417.0642074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 88 -
Rwork0.288 1175 -
obs--99.37 %
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)
11.93150.91440.11380.46560.14441.8448-0.09450.17920.1239-0.06210.11160.04010.0634-0.3184-0.01710.0241-0.04970.00470.1362-0.00930.01993.4261.25726.125
23.04261.5148-0.10621.34160.24483.49250.1528-0.33890.09190.0722-0.10130.263-0.0835-0.3964-0.05150.1396-0.07040.01540.1813-0.00010.112591.29262.91240.197
32.77780.32130.21934.3778-0.55939.30690.03680.12660.268-0.16820.08780.0346-0.2654-0.1524-0.12460.0869-0.0022-0.02770.01870.00660.0603105.79472.02735.765
43.82561.60271.6760.91610.72271.94870.0611-0.36670.12230.1384-0.16440.10860.1582-0.36520.10320.1002-0.04410.01680.0925-0.00850.029593.95461.43744.809
511.9696-1.2988-0.73975.09230.06796.7690.1833-0.17850.79890.1624-0.09740.5262-0.0818-1.0613-0.08580.1007-0.10660.03950.312-0.02620.129676.64455.3539.149
67.773-2.083.21515.483210.931810.73330.3029-0.5183-0.95270.1147-0.09470.56960.4327-0.4766-0.20820.3092-0.1898-0.11040.2090.11970.195275.48245.940.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 99
2X-RAY DIFFRACTION2A100 - 131
3X-RAY DIFFRACTION3A132 - 154
4X-RAY DIFFRACTION4A155 - 188
5X-RAY DIFFRACTION5A189 - 215
6X-RAY DIFFRACTION6A216 - 231

+
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