[English] 日本語
Yorodumi
- PDB-8f9h: H64A swMb-MeNO adduct -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f9h
TitleH64A swMb-MeNO adduct
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Myoglobin / Nitroso / Nitrosomethane / RNO / Mb
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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITROSOMETHANE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHerrera, V.E. / Thomas, L.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1566509 United States
National Science Foundation (NSF, United States)CHE-1213674 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
CitationJournal: Biochemistry / Year: 2023
Title: Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives.
Authors: Herrera, V.E. / Charles, T.P. / Scott, T.G. / Prather, K.Y. / Nguyen, N.T. / Sohl, C.D. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionNov 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0564
Polymers17,2981
Non-polymers7583
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, UV-Vis spectroscopy supported ligand bound swMb-MeNO
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-29 kcal/mol
Surface area7820 Å2
Unit cell
Length a, b, c (Å)34.856, 29.027, 64.263
Angle α, β, γ (deg.)90.000, 105.890, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#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 BL21(DE3) (bacteria) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NSM / NITROSOMETHANE


Mass: 45.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 296.3 K / Method: batch mode / pH: 7.4
Details: 2.3-2.6 M Ammonium Sulfate, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4
Temp details: Room temperature, could fluctuate slightly day by day

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50.01 Å / Num. obs: 12746 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.053 / Net I/σ(I): 22.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.7820.0985620.9650.0790.1270.67292.9
1.78-1.812.40.16600.9550.0770.1270.77598.8
1.81-1.852.60.0956160.9760.0690.1180.81699.4
1.85-1.8930.0916160.9780.0610.1110.70699
1.89-1.933.40.0896420.9790.0550.1050.84799.5
1.93-1.973.90.0816280.9840.0470.0940.71299.8
1.97-2.023.90.0856310.9830.0480.0980.868100
2.02-2.0740.0766570.9870.0430.0880.879100
2.07-2.144.20.076130.9860.0380.080.836100
2.14-2.24.20.0626400.9910.0340.0710.74399.8
2.2-2.284.40.0666390.9920.0350.0750.995100
2.28-2.384.40.0586340.9920.0310.0660.69499.8
2.38-2.484.30.0546470.9930.0280.0610.712100
2.48-2.614.40.0526380.9930.0270.0590.721100
2.61-2.784.30.0496310.9940.0260.0550.728100
2.78-2.994.30.0476450.9940.0250.0530.769100
2.99-3.294.30.0426470.9940.0220.0480.78499.8
3.29-3.774.20.0396570.9940.0210.0441.06599.8
3.77-4.7540.0366560.9940.0190.0411.10299.5
4.75-503.40.0276870.9970.0160.0320.78199.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ILE

5ile


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.167 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 619 4.9 %RANDOM
Rwork0.1522 ---
obs0.1545 12074 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.27 Å2 / Biso mean: 18.131 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.01 Å2
2--0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 51 85 1334
Biso mean--14.89 22.38 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191283
X-RAY DIFFRACTIONr_bond_other_d0.0020.021228
X-RAY DIFFRACTIONr_angle_refined_deg2.062.0071735
X-RAY DIFFRACTIONr_angle_other_deg1.08332844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83424.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.519154
X-RAY DIFFRACTIONr_chiral_restr0.1470.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021394
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02259
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 39 -
Rwork0.204 837 -
all-876 -
obs--95.22 %

+
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