[English] 日本語
Yorodumi
- PDB-2flh: Crystal structure of cytokinin-specific binding protein from mung... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2flh
TitleCrystal structure of cytokinin-specific binding protein from mung bean in complex with cytokinin
Componentscytokinin-specific binding protein
KeywordsPLANT PROTEIN / cytokinins / zeatin / pathogenesis-related proteins / multiple-ligand binding
Function / homology
Function and homology information


cytokinin binding / gibberellin binding / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / : / Phytohormone-binding protein CSBP
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsPasternak, O. / Bujacz, G.D. / Sikorski, M.M. / Jaskolski, M.
Citation
Journal: Plant Cell / Year: 2006
Title: Crystal Structure of Vigna radiata Cytokinin-Specific Binding Protein in Complex with Zeatin.
Authors: Pasternak, O. / Bujacz, G.D. / Fujimoto, Y. / Hashimoto, Y. / Jelen, F. / Otlewski, J. / Sikorski, M.M. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary crystallographic studies of mung bean cytokinin-specific binding protein
Authors: Bujacz, G. / Pasternak, O. / Fujimoto, Y. / Hashimoto, Y. / Sikorski, M.M. / Jaskolski, M.
#2: Journal: Eur.J.Biochem. / Year: 1998
Title: Purification and cDNA cloning of cytokinin-specific binding protein from mung bean (Vigna radiata)
Authors: Fujimoto, Y. / Nagata, R. / Fukasawa, H. / Yano, K. / Azuma, M. / Iida, A. / Sugimoto, S. / Shudo, K. / Hashimoto, Y.
#3: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two homologous pathogenesis-related proteins from yellow lupine
Authors: Biesiadka, J. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a yellow lupine pathogenesis-related PR-10 protein belonging to a novel subclass
Authors: Pasternak, O. / Biesiadka, J. / Dolot, R. / Handschuh, L. / Bujacz, G. / Sikorski, M.M. / Jaskolski, M.
#5: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-ray and NMR structure of Bet v 1, the origin of birch pollen allergy.
Authors: Gajhede, M. / Osmark, P. / Poulsen, F.M. / Ipsen, H. / Larsen, J.N. / van Neerven, R.J.J. / Schou, C. / Lowenstein, H. / Spangford, M.D.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The het group ZEA is also known as (E)-6-(4-HYDROXY-3- METHYL-BUT-2-ENYLAMINO)PURINE
Remark 999SEQUENCE According to authors, there is an error in the GB entry GB 4190976 at position 92 (Asn ...SEQUENCE According to authors, there is an error in the GB entry GB 4190976 at position 92 (Asn instead of Ser)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cytokinin-specific binding protein
B: cytokinin-specific binding protein
C: cytokinin-specific binding protein
D: cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47115
Polymers70,4514
Non-polymers2,01911
Water11,620645
1
A: cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2714
Polymers17,6131
Non-polymers6583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0744
Polymers17,6131
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0744
Polymers17,6131
Non-polymers4613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: cytokinin-specific binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0513
Polymers17,6131
Non-polymers4382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.790, 113.790, 86.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe biological assembly is a monomer.

-
Components

#1: Protein
cytokinin-specific binding protein


Mass: 17612.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: vrcsbp / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4190976, UniProt: A0A1S3THR8*PLUS
#2: Chemical
ChemComp-ZEA / (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol / TRANS-ZEATIN


Mass: 219.243 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H13N5O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 292 K / pH: 7.5
Details: sodium citrate, HEPES, zeatin, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.844, 1.2547, 1.2580, 1.2703
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2002 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8441
21.25471
31.2581
41.27031
ReflectionResolution: 1.2→30 Å / Num. obs: 189769 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.6 / % possible all: 93.2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC DISPLACEMENT PARAMETERS. H ATOMS AT RIDING POSITIONS. SEVERAL RESIDUES COULD NOT BE MODELED AT THE C-TERMINI (152-155 IN A, 154-155 IN B, 153-155 IN C, 155 IN A) AND IN ONE LOOP ...Details: ANISOTROPIC DISPLACEMENT PARAMETERS. H ATOMS AT RIDING POSITIONS. SEVERAL RESIDUES COULD NOT BE MODELED AT THE C-TERMINI (152-155 IN A, 154-155 IN B, 153-155 IN C, 155 IN A) AND IN ONE LOOP OF MOLECULE A (123-129). LONG SIDE CHAINS OF SOME SURFACE RESIDUES WERE POORLY VISIBLE IN ELECTRON DENSITY MAPS AND WERE MODELED WITH 0.0 OCCUPANCY
RfactorNum. reflectionSelection details
Rfree0.19 2242 RANDOM
all0.16 189657 -
obs0.157 189657 -
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 22.1 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5033 0 146 676 5855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d2.229
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

+
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