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- PDB-4it8: A sperm whale myoglobin mutant L29H Mb with two distal histidines -

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Basic information

Entry
Database: PDB / ID: 4it8
TitleA sperm whale myoglobin mutant L29H Mb with two distal histidines
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / L29H mutation / alpha helix holding / NO2 reductase / 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 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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, Y.-W. / Tan, X.-S. / Li, W. / Sun, M.-H. / Wen, G.-B. / Liu, J.-H.
CitationJournal: RSC Adv / Year: 2013
Title: Structural and nitrite reductase activity comparisons of myoglobins with one to three distal histidines.
Authors: Sun, M.-H. / Li, W. / Liu, J.-H. / Wen, G.-B. / Tan, X.-S. / Lin, Y.-W.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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)18,0082
Polymers17,3911
Non-polymers6161
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.899, 48.433, 78.923
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: 17391.137 Da / Num. of mol.: 1 / Mutation: L29H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pET22b(+) / 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.: 222 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8,000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→35.607 Å / Num. obs: 25185 / % possible obs: 14.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 7.2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.006 / Rsym value: 0.133 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.5-1.53199.7
1.53-1.55199.8
1.55-1.58199.9
1.58-1.62199.9
1.62-1.65199.9
1.65-1.69199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Myoglobin L29H/F43H mutant

Resolution: 1.5→35.607 Å / SU ML: 0.29 / σ(F): 0.14 / Phase error: 16.15 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1866 2000 8.07 %
Rwork0.1717 --
obs0.1729 24798 98.44 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.624 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3768 Å2-0 Å20 Å2
2---0.322 Å2-0 Å2
3---2.6988 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 43 222 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011297
X-RAY DIFFRACTIONf_angle_d1.3671757
X-RAY DIFFRACTIONf_dihedral_angle_d13.367482
X-RAY DIFFRACTIONf_chiral_restr0.07181
X-RAY DIFFRACTIONf_plane_restr0.005214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53740.20681360.17211546X-RAY DIFFRACTION95
1.5374-1.57890.17551380.16581580X-RAY DIFFRACTION97
1.5789-1.62540.21281400.15911584X-RAY DIFFRACTION98
1.6254-1.67780.19161390.1661586X-RAY DIFFRACTION97
1.6778-1.73780.1761410.16661607X-RAY DIFFRACTION98
1.7378-1.80740.1931400.15841605X-RAY DIFFRACTION98
1.8074-1.88960.18261410.15971605X-RAY DIFFRACTION99
1.8896-1.98930.18141420.1641622X-RAY DIFFRACTION99
1.9893-2.11390.18911450.17391648X-RAY DIFFRACTION100
2.1139-2.27710.16371430.16121629X-RAY DIFFRACTION100
2.2771-2.50620.17331470.16151675X-RAY DIFFRACTION100
2.5062-2.86870.19751460.17661666X-RAY DIFFRACTION100
2.8687-3.61370.19031460.1751672X-RAY DIFFRACTION99
3.6137-35.61750.19051560.18981773X-RAY DIFFRACTION99

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