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- PDB-1dtm: CRYSTAL STRUCTURE OF THE SPERM-WHALE MYOGLOBIN MUTANT H93G COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1dtm
TitleCRYSTAL STRUCTURE OF THE SPERM-WHALE MYOGLOBIN MUTANT H93G COMPLEXED WITH 4-METHYLIMIDAZOLE, METAQUO FORM
ComponentsRECOMBINANT SPERM WHALE MYOGLOBIN VARIANT H93G
KeywordsOXYGEN STORAGE/TRANSPORT / Heme protein / Myoglobin / ligand-substitution / OXYGEN STORAGE-TRANSPORT COMPLEX
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
4-METHYLIMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2.13 Å
AuthorsBarrick, D. / Dahlquist, F.W.
Citation
Journal: Proteins / Year: 2000
Title: Trans-substitution of the proximal hydrogen bond in myoglobin: I. Structural consequences of hydrogen bond deletion.
Authors: Barrick, D. / Dahlquist, F.W.
#1: Journal: To be Published
Title: Trans-substitution of the proximal hydrogen bond in myoglobin: II. Energetics, functional consequences, and implications for hemoglobin allostery
Authors: Barrick, D.
History
DepositionJan 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECOMBINANT SPERM WHALE MYOGLOBIN VARIANT H93G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8523
Polymers17,1541
Non-polymers6992
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.276, 48.892, 78.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RECOMBINANT SPERM WHALE MYOGLOBIN VARIANT H93G


Mass: 17153.857 Da / Num. of mol.: 1 / Mutation: H93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: PMB413B / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#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-4MZ / 4-METHYLIMIDAZOLE


Mass: 82.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6N2
Details: 4-methylimidazole from Aldrich Chemical Company (Cat # 19,988-5). 4-methylimidazole substituted for imidazole by extensive buffer exchange using spin-columns equilibrated with 0.1 M 4-methylimidazole.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 35 % PEG 8000, 0.3-0.35 M NaOAc, 0.1 M PIPES, and 0.1 % dioxane, 0.1 M 4-methylimidazole, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Temp details: Room temperature
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 %Mb solution1drop
235-37.5 %PEG80001reservoir
30.3-0.35 M1reservoirNaOAc
40.1 MPIPES1reservoir
50.1 %dioxane1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jul 29, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. all: 7356 / Num. obs: 7356 / % possible obs: 78.9 % / Redundancy: 2.63 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 12.54
Reflection shellResolution: 2.13→2.298 Å / Redundancy: 1.51 % / Rmerge(I) obs: 0.141 / Num. unique all: 853 / % possible all: 49
Reflection shell
*PLUS
% possible obs: 49 %

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing
RefinementResolution: 2.13→20 Å
Stereochemistry target values: Bond length rmsd 0.02 angstroms, Bond angle 3.0 degrees, B-correlation 6 square angstroms, Trigonal planarity 0.02, Planar groups 0.02
Details: 4-methyl imidazole built into an omit map in the proximal pocket after extensive all-atom refinement of the protein and heme
RfactorNum. reflection% reflection
all0.175 7356 -
obs0.175 7356 79 %
Refinement stepCycle: LAST / Resolution: 2.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 49 15 1240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.9
X-RAY DIFFRACTIONt_bond_d0.019

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