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- PDB-3vm9: Dimeric horse myoglobin -

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Basic information

Entry
Database: PDB / ID: 3vm9
TitleDimeric horse myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / oxygen binding / oxygen transport
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Helix Hairpins - #2100 / Helix Hairpins - #2110 / Helix Hairpins / Myoglobin / Globin family profile. / Globin / Globin / Helix non-globular / Globin-like superfamily / Special
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN ATOM / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsNagao, S. / Osuka, H. / Yamada, T. / Uni, T. / Shomura, Y. / Imai, K. / Higuchi, Y. / Hirota, S.
CitationJournal: Dalton Trans / Year: 2012
Title: Structural and oxygen binding properties of dimeric horse myoglobin
Authors: Nagao, S. / Osuka, H. / Yamada, T. / Uni, T. / Shomura, Y. / Imai, K. / Higuchi, Y. / Hirota, S.
History
DepositionDec 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2326
Polymers33,9672
Non-polymers1,2654
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-96 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.340, 62.523, 83.354
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: 16983.514 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#2: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 6000, 200mM CH3COONa, 0.1M Tris-HCl buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 9, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→20 Å / Num. all: 139690 / Num. obs: 139129 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 7.4 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6909 / % possible all: 99.5

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Processing

Software
NameClassification
BSSdata collection
MOLREPphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WLA

1wla


Resolution: 1.05→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.168 6918 RANDOM
obs0.128 133007 -
all-139129 -
Refinement stepCycle: LAST / Resolution: 1.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 88 638 3124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.088

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