[English] 日本語
Yorodumi
- PDB-5vzo: Sperm whale myoglobin H64A with nitric oxide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vzo
TitleSperm whale myoglobin H64A with nitric oxide
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / nitrosyl / nitric oxide
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
Model detailsThis stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine.
AuthorsWang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1213674 United States
CitationJournal: Biochemistry / Year: 2018
Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.
Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / Richter-Addo, G.B.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,73915
Polymers17,2981
Non-polymers1,44114
Water2,990166
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-42 kcal/mol
Surface area8150 Å2
2
A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules

A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,21745
Polymers51,8943
Non-polymers4,32342
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area11320 Å2
ΔGint-168 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.222, 90.222, 45.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-206-

SO4

21A-206-

SO4

31A-455-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17298.094 Da / Num. of mol.: 1 / Mutation: H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185

-
Non-polymers , 6 types, 180 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 0.1 M Tris-Hcl, 1 mM EDTA, pH 9 2.3 M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 20265 / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Χ2: 2.48 / Net I/av σ(I): 54.952 / Net I/σ(I): 23.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.813.60.0910.9870.0550.1071.51893.5
1.81-1.844.20.0870.990.0480.0991.67499.8
1.84-1.884.80.0870.9920.0440.0981.726100
1.88-1.925.60.0830.9940.0390.0921.776100
1.92-1.965.80.0810.9940.0370.0891.957100
1.96-25.80.0740.9940.0330.0811.977100
2-2.0560.0720.9950.0310.0782.177100
2.05-2.116.10.0690.9960.030.0752.424100
2.11-2.176.20.0650.9960.0280.0712.359100
2.17-2.246.40.0650.9960.0270.072.516100
2.24-2.326.40.0610.9960.0260.0662.581100
2.32-2.426.50.060.9960.0250.0652.588100
2.42-2.536.40.0610.9960.0260.0662.787100
2.53-2.666.40.060.9960.0260.0652.853100
2.66-2.836.40.0580.9970.0250.0632.781100
2.83-3.046.40.0550.9950.0240.062.842100
3.04-3.356.40.050.9970.0210.0542.751100
3.35-3.836.30.0470.9970.020.0522.87199.7
3.83-4.836.10.0490.9970.0210.0543.16999.8
4.83-505.60.0460.9980.0210.0513.01197.3

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.2data extraction
RefinementResolution: 1.78→29.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.633 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 1034 5.1 %RANDOM
Rwork0.1487 ---
obs0.1506 19212 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.55 Å2 / Biso mean: 16.282 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.06 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.78→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 93 166 1471
Biso mean--25.93 24.31 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191354
X-RAY DIFFRACTIONr_bond_other_d0.0020.021307
X-RAY DIFFRACTIONr_angle_refined_deg2.1862.0171824
X-RAY DIFFRACTIONr_angle_other_deg0.97933014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1235158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38224.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.787154
X-RAY DIFFRACTIONr_chiral_restr0.1510.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021477
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02307
X-RAY DIFFRACTIONr_mcbond_it1.371.256624
X-RAY DIFFRACTIONr_mcbond_other1.3191.254622
X-RAY DIFFRACTIONr_mcangle_it1.8371.874781
LS refinement shellResolution: 1.783→1.829 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 87 -
Rwork0.179 1409 -
all-1496 -
obs--99.8 %

+
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