[English] 日本語
Yorodumi
- PDB-2xyk: Group II 2-on-2 Hemoglobin from the Plant Pathogen Agrobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xyk
TitleGroup II 2-on-2 Hemoglobin from the Plant Pathogen Agrobacterium tumefaciens
Components2-ON-2 HEMOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX / 2/2 HEMOGLOBIN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Two-on-two hemoglobin-3 / Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin
Similarity search - Component
Biological speciesAGROBACTERIUM TUMEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPesce, A. / Nardini, M. / LaBarre, M. / Richard, C. / Wittenberg, J.B. / Wittenberg, B.A. / Guertin, M. / Bolognesi, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2011
Title: Structural Characterization of a Group II 2/2 Hemoglobin from the Plant Pathogen Agrobacterium Tumefaciens.
Authors: Pesce, A. / Nardini, M. / Labarre, M. / Richard, C. / Wittenberg, J.B. / Wittenberg, B.A. / Guertin, M. / Bolognesi, M.
History
DepositionNov 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 2-ON-2 HEMOGLOBIN
B: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7464
Polymers30,5132
Non-polymers1,2332
Water1,78399
1
A: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8732
Polymers15,2561
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 2-ON-2 HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8732
Polymers15,2561
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.180, 44.491, 57.580
Angle α, β, γ (deg.)90.00, 112.16, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2-ON-2 HEMOGLOBIN


Mass: 15256.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AGROBACTERIUM TUMEFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7CX73
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.07 Å3/Da / Density % sol: 40.51 % / Description: NONE
Crystal growpH: 8.5
Details: 45% W/V PEG 4,000, LITHIUM CHLORIDE 0.8 M AND TRIS-HCL 0.1 M, PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→34.2 Å / Num. obs: 14775 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.6 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NGK

1ngk


Resolution: 2.1→33.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.864 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NO ELECTRON DENSITY WAS OBSERVED FOR THE LAST 4 C- TERMINAL RESIDUES OF CHAIN A, AND FOR THE LAST 3 C-TERMINAL RESIDUES OF CHAIN B.
RfactorNum. reflection% reflectionSelection details
Rfree0.23856 1512 10.2 %RANDOM
Rwork0.17702 ---
obs0.18323 13255 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.33 Å2
2--0.2 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.1→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 86 99 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3772.0783044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74722.039103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68115347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0851523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021737
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21019
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21488
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0210.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1341.51336
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63222074
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.77531038
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9734.5966
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 116 -
Rwork0.205 950 -
obs--99.91 %

+
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