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- PDB-3m38: The roles of Glutamates and Metal ions in a rationally designed n... -

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Basic information

Entry
Database: PDB / ID: 3m38
TitleThe roles of Glutamates and Metal ions in a rationally designed nitric oxide reductase based on myoglobin: I107E FeBMb (No metal ion binding to FeB site)
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Alpha Helix / Heme protein / Metal-binding / NO reductase
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 domain profile. / Globin-like / Globin / Globin / 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 / SYNCHROTRON / AB INITIO / Resolution: 1.42 Å
AuthorsLin, Y.-W. / Yeung, N. / Gao, Y.-G. / Miner, K.D. / Tian, S. / Robinson, H. / Lu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin.
Authors: Lin, Y.W. / Yeung, N. / Gao, Y.G. / Miner, K.D. / Tian, S. / Robinson, H. / Lu, Y.
History
DepositionMar 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations / Category: 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 1.3Feb 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9132
Polymers17,2971
Non-polymers6161
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.850, 46.980, 77.670
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


Mass: 17296.854 Da / Num. of mol.: 1 / Mutation: L30H, F43H, V69E, I107E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: Plasmid pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.56 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.089 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.089 Å / Relative weight: 1
ReflectionResolution: 1.42→40.95 Å / Num. obs: 24766 / Rmerge(I) obs: 0.041

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.42→10 Å / Num. parameters: 5835 / Num. restraintsaints: 5202 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
all0.2194 26192 --
obs-24766 93.6 %-
Rfree---RANDOM
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1455
Refinement stepCycle: LAST / Resolution: 1.42→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 43 191 1454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0244
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps0

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