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- PDB-2mgb: HIGH RESOLUTION CRYSTAL STRUCTURES OF FIVE DISTAL HISTIDINE MUTAN... -

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Basic information

Entry
Database: PDB / ID: 2mgb
TitleHIGH RESOLUTION CRYSTAL STRUCTURES OF FIVE DISTAL HISTIDINE MUTANTS OF SPERM WHALE MYOGLOBIN
ComponentsMYOGLOBIN
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Globin / Myoglobin / Globin-like superfamily / Globin/Protoglobin / Globin / Globin family profile.
Myoglobin
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsQuillin, M.L. / Arduini, R.M. / Phillips Jr., G.N.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin.
Authors: Quillin, M.L. / Arduini, R.M. / Olson, J.S. / Phillips Jr., G.N.
#1: Journal: Proteins / Year: 1990
Title: Crystal Structure of Myoglobin from a Synthetic Gene
Authors: Phillips Jr., G.N. / Arduini, R.M. / Springer, B.A. / Sligar, S.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: High-Level Expression of Sperm Whale Myoglobin in Escherichia Coli
Authors: Springer, B.A. / Sligar, S.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 10, 1993-
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)17,9973
Polymers17,2841
Non-polymers7132
Water3,261181
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)91.200, 91.200, 45.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Atom site foot note1: THIS OXYGEN IS A WATER MOLECULE COORDINATED TO FE IN THE HEM GROUP.

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Components

#1: Protein/peptide MYOGLOBIN /


Mass: 17284.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: SYNTHETIC GENE / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Heme
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.38 %
Crystal grow
*PLUS
pH: 9 / Method: batch method / Details: micro seeding
Components of the solutions
*PLUS

Crystal-ID: 1 / Sol-ID: 1

IDConc.Common name
160 mg/mlprotein
22.4 Mammonium sulfate
315 mMTris-HCl
40.75 mMEDTA

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementResolution: 2→5 Å /
RfactorNum. reflection
Obs0.155 12934
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 49 180 1448
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal target
p_bond_d0.0190.02
p_angle_d0.0340.03
p_angle_deg
p_planar_d0.0610.06
p_hb_or_metal_coord
p_mcbond_it1.4981.5
p_mcangle_it2.1642
p_scbond_it2.9582
p_scangle_it4.4513
p_plane_restr0.0270.03
p_chiral_restr0.1920.15
p_singtor_nbd0.1960.5
p_multtor_nbd0.2380.5
p_xhyhbond_nbd0.3040.5
p_xyhbond_nbd
p_planar_tor3.53
p_staggered_tor16.815
p_orthonormal_tor37.620
p_transverse_tor
p_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 5 Å / Num. reflection obs: 12934 / Rfactor obs: 0.155

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