5M3S | pdb_00005m3s

Low-dose fixed target serial synchrotron crystallography structure of Metmyoglobin

• PDB DOI: https://doi.org/10.2210/pdb5M3S/pdb

• Classification: OXYGEN BINDING
• Organism(s): Physeter macrocephalus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-17 Released: 2016-12-14 
• Deposition Author(s): Axford, D., Owen, R.L., Sherrell, D., Muller-Werkmeister, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Low-dose fixed-target serial synchrotron crystallography.

Owen, R.L., Axford, D., Sherrell, D.A., Kuo, A., Ernst, O.P., Schulz, E.C., Miller, R.J., Mueller-Werkmeister, H.M.

(2017) Acta Crystallogr D Struct Biol 73: 373-378

• PubMed: 28375148 
• DOI: https://doi.org/10.1107/S2059798317002996
• Primary Citation Related Structures: 
  5M3S, 5O41


• PubMed Abstract: 
  

  The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption.

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Organizational Affiliation: 
• Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England.
Department of Biochemistry, University of Toronto, King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 18.37 kDa 
• Atom Count: 1,510 
• Modeled Residue Count: 154 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter macrocephalus	Mutation(s): 0  Gene Names: MB EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185  Go to UniProtKB:  P02185

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.225 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.436	α = 90
b = 91.436	β = 90
c = 45.957	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
cctbx.prime	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Axford, D., Owen, R.L., Sherrell, D., Muller-Werkmeister, H.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2017-04-19
  Changes: Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description