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- PDB-1duk: WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1duk
TitleWILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN
ComponentsWILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN
KeywordsOXYGEN STORAGE/TRANSPORT / Oxygen-storage protein / myoglobin / heme protein / 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
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 17, 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 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8512
Polymers17,2351
Non-polymers6161
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.132, 49.071, 79.339
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 WILD-TYPE RECOMBINANT SPERM WHALE METAQUOMYOGLOBIN


Mass: 17234.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FERRIC PROTOPORPHYRIN IX BOUND DURING BACTERIAL EXPRESSION OF THE PROTEIN
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 45.72 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 35 % PEG 8000, 0.3 M NaOAc, 0.1 M PIPES, VAPOR DIFFUSION, HANGING DROP
Temp details: Room temperature
Crystal grow
*PLUS
pH: 6.5
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

DiffractionAmbient temp details: Room temperature
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 11, 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: 7405 / Num. obs: 7405 / % possible obs: 78 % / Redundancy: 2.21 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 7.74
Reflection shellResolution: 2.13→2.29 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.163 / Num. unique all: 838 / % possible all: 47
Reflection shell
*PLUS
% possible obs: 47 %

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing
RefinementResolution: 2.13→20 Å
Stereochemistry target values: Bond lengths 0.02 rms; bond angles 3 degrees rms, trig planes 0.02 rms; general planes 0.02 rms; B-correlation 6.0 square angstroms rms.
RfactorNum. reflection% reflection
all0.18 7405 -
obs0.18 7405 78 %
Refinement stepCycle: LAST / Resolution: 2.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 43 12 1267
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3

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