[English] 日本語
Yorodumi
- PDB-4nzi: Crystal structure of murine neuroglobin mutant V140W -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nzi
TitleCrystal structure of murine neuroglobin mutant V140W
ComponentsNeuroglobin
KeywordsTRANSPORT PROTEIN / Globin / oxygen transporter
Function / homology
Function and homology information


Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / cellular response to hydrogen peroxide / oxygen binding / neuron projection development / cellular response to hypoxia ...Intracellular oxygen transport / GDP-dissociation inhibitor activity / nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / oxygen carrier activity / cellular response to hydrogen peroxide / oxygen binding / neuron projection development / cellular response to hypoxia / perikaryon / response to hypoxia / mitochondrial matrix / apoptotic process / heme binding / negative regulation of apoptotic process / metal ion binding / cytosol
Similarity search - Function
Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neuroglobin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAvella, G. / Savino, C. / Vallone, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Engineering the internal cavity of neuroglobin demonstrates the role of the haem-sliding mechanism.
Authors: Avella, G. / Ardiccioni, C. / Scaglione, A. / Moschetti, T. / Rondinelli, C. / Montemiglio, L.C. / Savino, C. / Giuffre, A. / Brunori, M. / Vallone, B.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Neuroglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1063
Polymers17,3941
Non-polymers7132
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.214, 87.214, 114.399
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-333-

HOH

-
Components

#1: Protein Neuroglobin /


Mass: 17393.650 Da / Num. of mol.: 1 / Mutation: C55S, C120S, V140W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngb / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ER97
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulphate, 0.1M MES, 10% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.86437 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2012
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.86437 Å / Relative weight: 1
ReflectionResolution: 2.1→45.6 Å / Num. all: 19925 / Num. obs: 9964 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Biso Wilson estimate: 31.06 Å2
Reflection shellResolution: 2.1→2.175 Å / % possible all: 97.97

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.599 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.7917 / SU ML: 0.61 / σ(F): 1.38 / Phase error: 27.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 987 9.91 %Random
Rwork0.219 ---
obs0.2233 9962 99.73 %-
all-9964 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.259 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 106.53 Å2 / Biso mean: 39.7681 Å2 / Biso min: 11.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.8434 Å2-0 Å20 Å2
2---0.8434 Å2-0 Å2
3---1.6868 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 48 35 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091361
X-RAY DIFFRACTIONf_angle_d1.2661876
X-RAY DIFFRACTIONf_chiral_restr0.077185
X-RAY DIFFRACTIONf_plane_restr0.005230
X-RAY DIFFRACTIONf_dihedral_angle_d19.486493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.21070.33291430.26841227137098
2.2107-2.34920.31951410.257612781419100
2.3492-2.53060.31011350.247712691404100
2.5306-2.78520.32241390.250212631402100
2.7852-3.18820.28941410.24112851426100
3.1882-4.01640.24921420.202813031445100
4.0164-45.60990.20231460.185813501496100

+
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