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- PDB-1duo: SPERM WHALE METAQUOMYOGLOBIN PROXIMAL HISTIDINE MUTANT H93G WITH ... -

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Basic information

Entry
Database: PDB / ID: 1duo
TitleSPERM WHALE METAQUOMYOGLOBIN PROXIMAL HISTIDINE MUTANT H93G WITH 1-METHYLIMIDAZOLE AS PROXIMAL LIGAND.
ComponentsSPERM WHALE METAQUOMYOGLOBIN VARIANT H93G
KeywordsOXIDOREDUCTASE / Myoglobin / ligand substitution / heme protein
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
1-METHYLIMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2 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 18, 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 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0May 15, 2019Group: Atomic model / Data collection / Source and taxonomy / Category: atom_site / pdbx_entity_src_syn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z
Revision 2.1Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPERM WHALE METAQUOMYOGLOBIN VARIANT H93G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8533
Polymers17,1541
Non-polymers7002
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.161, 49.033, 79.240
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 SPERM WHALE METAQUOMYOGLOBIN VARIANT H93G


Mass: 17153.857 Da / Num. of mol.: 1 / Mutation: H93G
Source method: isolated from a genetically manipulated source
Details: HEME IS BOUND TO THE PROTEIN DURING BACTERIAL EXPRESSION
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: P413B / 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-1MZ / 1-METHYLIMIDAZOLE


Mass: 83.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 35 % PEG 8000, 0.3 M NaOAc, 0.1 M PIPES, and 0.1 % dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Temp details: Room temperature
Crystal grow
*PLUS
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: Nov 29, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 9290 / Num. obs: 9290 / % possible obs: 76 % / Redundancy: 2.19 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.15 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.182 / Num. unique all: 1522 / % possible all: 71.1
Reflection shell
*PLUS
% possible obs: 71.1 %

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
SDMSdata scaling
TNTphasing
RefinementResolution: 2→20 Å
Stereochemistry target values: Bond length 0.02 angstroms; Bond angles 3 degrees; Trig planes 0.02, General planes 0.02; B-correlation 6.0 angstroms squared.
RfactorNum. reflection% reflection
Rwork0.181 --
all-9290 -
obs-9290 76 %
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 49 24 1251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3

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