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- PDB-1irc: CYSTEINE RICH INTESTINAL PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1irc
TitleCYSTEINE RICH INTESTINAL PROTEIN
ComponentsMYOGLOBIN (METAQUO)
KeywordsOXYGEN STORAGE / RESPIRATORY PROTEIN / HEME
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 / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 2.17 Å
AuthorsBarrick, D.E. / Feese, M.
Citation
Journal: Biochemistry / Year: 1994
Title: Replacement of the proximal ligand of sperm whale myoglobin with free imidazole in the mutant His-93-->Gly.
Authors: Barrick, D.
#1: Journal: Biochemistry / Year: 1994
Title: Replacement of the Proximal Ligand of Sperm Whale Myoglobin with Free Imidazole in the Mutant His-93-->Gly
Authors: Barrick, D.
History
DepositionDec 19, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYOGLOBIN (METAQUO)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9713
Polymers17,2851
Non-polymers6862
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.150, 49.040, 79.140
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 MYOGLOBIN (METAQUO)


Mass: 17285.053 Da / Num. of mol.: 1 / Mutation: H93G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: SPERM WHALE MYOGLOBIN SYNTHETI / Plasmid: PMB413B WITH HISTIDINE 93 REPLACED WITH GLYCINE
Gene (production host): SPERM WHALE MYOGLOBIN SYNTHETIC GENE
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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Source detailsTHE PROTEIN WAS PRODUCED USING AN ESCHERICHIA COLI EXPRESSION SYSTEM OF SPRINGER AND SLIGAR [(1987) ...THE PROTEIN WAS PRODUCED USING AN ESCHERICHIA COLI EXPRESSION SYSTEM OF SPRINGER AND SLIGAR [(1987) PROC. NAT. ACAD. SCI. U.S.A. 84, 8961-8965], EXCEPT THAT THE ORIGINAL ASN CODON AT POSITION 122 OF THEIR GENE WAS REPLACED WITH ASP TO GIVE THE WILD TYPE SEQUENCE. IN ADDITION, THE PROTEIN LIKELY CONTAINS AN N-TERMINAL FORMYL-METHIONINE, ALTHOUGH THIS RESIDUE IS NOT WELL DETERMINED BY THE ELECTRON DENSITY. THE PROTEIN WAS PURIFIED AS DESCRIBED IN BARRICK, D. (1994) BIOCHEMISTRY 33, 6546-6554.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135 %PEG80001reservoir
2300 mM1reservoirNaOAc
30.1 MPIPES1reservoir
40.1 %dioxane1reservoir
56 mg/mlprotein1drop
65 mMimidazole1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 7676 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.033
Reflection
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 26.6 Å / Num. measured all: 25555

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
RefinementResolution: 2.17→20 Å / Num. reflection obs: 7171 / σ(F): 0 / Stereochemistry target values: PROTGEO.DAT
Refinement stepCycle: LAST / Resolution: 2.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 48 20 1236
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.9

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