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- PDB-5kkk: 1.7-Angstrom In situ Mylar structure of sperm whale myoglobin (SW... -

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Basic information

Entry
Database: PDB / ID: 5kkk
Title1.7-Angstrom In situ Mylar structure of sperm whale myoglobin (SWMb-CO) at 100 K
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBroecker, J. / Ernst, O.P.
Funding support Canada, Germany, 2items
OrganizationGrant numberCountry
Government of CanadaCanada Excellence Research Chair Canada
German Research Foundation (DFG)BR 5124/1-1 Germany
CitationJournal: Cryst Growth Des / Year: 2016
Title: A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals.
Authors: Broecker, J. / Klingel, V. / Ou, W.L. / Balo, A.R. / Kissick, D.J. / Ogata, C.M. / Kuo, A. / Ernst, O.P.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,56110
Polymers17,3651
Non-polymers1,1969
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.770, 90.770, 45.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-208-

CL

21A-517-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin


Mass: 17365.164 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 256 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.1 % / Description: cubes and rods
Crystal growTemperature: 293 K / Method: batch mode / pH: 9
Details: 10 mM Tris-HCl, 2.5 to 2.6 M (NH4)2SO4, 1 atm CO gas, seed solution in 10 mM Tris-HCl pH 9.0 and 3.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→24.91 Å / Num. obs: 22335 / % possible obs: 94 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.172 / Net I/σ(I): 4.35
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 1.24 / % possible all: 96

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHENIX1.9_1692refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+55 / Resolution: 1.7→24.905 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 22.51
RfactorNum. reflection% reflection
Rfree0.2149 2002 8.97 %
Rwork0.1758 --
obs0.1793 22329 93.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 72 247 1544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081392
X-RAY DIFFRACTIONf_angle_d1.0261895
X-RAY DIFFRACTIONf_dihedral_angle_d12.964521
X-RAY DIFFRACTIONf_chiral_restr0.061195
X-RAY DIFFRACTIONf_plane_restr0.004228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.40891430.36761481X-RAY DIFFRACTION96
1.7425-1.78960.31881410.29781466X-RAY DIFFRACTION96
1.7896-1.84230.2841450.23321471X-RAY DIFFRACTION96
1.8423-1.90170.27211470.221468X-RAY DIFFRACTION96
1.9017-1.96960.27391430.2151468X-RAY DIFFRACTION95
1.9696-2.04850.2281420.20441446X-RAY DIFFRACTION95
2.0485-2.14170.22391400.17971438X-RAY DIFFRACTION93
2.1417-2.25450.17971420.1711456X-RAY DIFFRACTION94
2.2545-2.39560.22371430.1581436X-RAY DIFFRACTION93
2.3956-2.58040.22611480.16591434X-RAY DIFFRACTION93
2.5804-2.83980.20311420.17981461X-RAY DIFFRACTION94
2.8398-3.24990.21671500.17221446X-RAY DIFFRACTION93
3.2499-4.09160.1781410.14451439X-RAY DIFFRACTION92
4.0916-24.90770.1881350.15361417X-RAY DIFFRACTION88

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