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- PDB-2in4: Crystal Structure of Myoglobin with Charge Neutralized Heme, ZnDMb-dme -

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Basic information

Entry
Database: PDB / ID: 2in4
TitleCrystal Structure of Myoglobin with Charge Neutralized Heme, ZnDMb-dme
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / globin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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
ZINC(II)-DEUTEROPORPHYRIN DIMETHYLESTER / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWheeler, K.E. / Nocek, J.M. / Cull, D.A. / Yatsunyk, L.A. / Rosenzweig, A.C. / Hoffman, B.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2007
Title: Dynamic docking of cytochrome b5 with myoglobin and alpha-hemoglobin: heme-neutralization "squares" and the binding of electron-transfer-reactive configurations.
Authors: Wheeler, K.E. / Nocek, J.M. / Cull, D.A. / Yatsunyk, L.A. / Rosenzweig, A.C. / Hoffman, B.M.
History
DepositionOct 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6843
Polymers16,9841
Non-polymers7002
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.604, 30.577, 56.485
Angle α, β, γ (deg.)90.00, 97.66, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiologica assembly is a monomer

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Components

#1: Protein Myoglobin


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HE5 / ZINC(II)-DEUTEROPORPHYRIN DIMETHYLESTER / ZND-DME


Mass: 604.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H34N4O4Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12-17 mg/ml protein solution, 3.3 M ammonium sulfate, 0.1 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.14→55.99 Å / Num. obs: 8041 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rsym value: 0.084
Reflection shellResolution: 2.14→2.203 Å / Redundancy: 5.4 % / Rsym value: 0.187 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YMB from PDB data base

1ymb


Resolution: 2.15→55.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.807 / SU ML: 0.152 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23191 373 4.6 %RANDOM
Rwork0.17538 ---
obs0.17807 8041 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.675 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0.14 Å2
2--0.46 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.15→55.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 87 97 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211332
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9912.0431819
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.40925.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48915230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.255152
X-RAY DIFFRACTIONr_chiral_restr0.0880.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021005
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2679
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2864
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.681.5778
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17221204
X-RAY DIFFRACTIONr_scbond_it1.6673658
X-RAY DIFFRACTIONr_scangle_it2.5934.5610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.203 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 20 -
Rwork0.193 518 -
obs--90.57 %

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