[English] 日本語
Yorodumi
- PDB-2r50: The crystal structure of nonsymbiotic corn hemoglobin 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r50
TitleThe crystal structure of nonsymbiotic corn hemoglobin 1
ComponentsNon-symbiotic hemoglobin
KeywordsMETAL BINDING PROTEIN / corn hemoglobin / plant hemoglobin / nonsymbiotic hemoglobin / Heme / Iron / Metal-binding
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors; With a cytochrome as acceptor / oxygen binding / oxidoreductase activity / heme binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...Leghaemoglobin, iron-binding site / Plant hemoglobins signature. / Leghaemoglobin / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Anaerobic nitrite reductase GLB1
Similarity search - Component
Biological speciesZea mays subsp. parviglumis (Balsas teosinte)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSmagghe, B.J. / Hoy, J.A. / Hargrove, M.S.
CitationJournal: To be Published
Title: The crystal structure of nonsymbiotic corn hemoglobin 1
Authors: Smagghe, B.J. / Hoy, J.A. / Hargrove, M.S.
History
DepositionSep 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Non-symbiotic hemoglobin
B: Non-symbiotic hemoglobin
C: Non-symbiotic hemoglobin
D: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,28415
Polymers73,2184
Non-polymers3,06611
Water10,521584
1
A: Non-symbiotic hemoglobin
D: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0947
Polymers36,6092
Non-polymers1,4855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
MethodPISA
2
B: Non-symbiotic hemoglobin
C: Non-symbiotic hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1908
Polymers36,6092
Non-polymers1,5816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.754, 89.734, 157.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Non-symbiotic hemoglobin / Hbt / ZEAmp GLB1


Mass: 18304.375 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays subsp. parviglumis (Balsas teosinte)
Species: Zea mays / Strain: subsp. parviglumis / Gene: HB, GLB1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21* DE3 / References: UniProt: Q9M593
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M Sodium Acetate, 0.2M Ammonium Sulfate, 20% PEG MME 1900, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 23, 2004 / Details: Osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→80 Å / Num. obs: 35371 / % possible obs: 99.6 % / Redundancy: 6.67 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.4 / Num. unique all: 2504 / % possible all: 97.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
AMoREphasing
REFMAC5.1.24refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1D8U

1d8u


Resolution: 2.2→79.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.762 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1873 5 %RANDOM
Rwork0.201 ---
obs0.203 35371 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.837 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.19 Å20 Å2
3----2.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4579 0 197 592 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224890
X-RAY DIFFRACTIONr_bond_other_d0.0080.024543
X-RAY DIFFRACTIONr_angle_refined_deg1.7792.0176626
X-RAY DIFFRACTIONr_angle_other_deg1.052310540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.645576
X-RAY DIFFRACTIONr_chiral_restr0.1110.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025351
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02993
X-RAY DIFFRACTIONr_nbd_refined0.2320.21428
X-RAY DIFFRACTIONr_nbd_other0.2530.25248
X-RAY DIFFRACTIONr_nbtor_other0.0940.22573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2266
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.215
X-RAY DIFFRACTIONr_mcbond_it1.3691.52906
X-RAY DIFFRACTIONr_mcangle_it2.4924618
X-RAY DIFFRACTIONr_scbond_it3.25431984
X-RAY DIFFRACTIONr_scangle_it5.2214.52008
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.319 126
Rwork0.264 2504
all-2630

+
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