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- PDB-4pq6: A sperm whale myoglobin single mutant L29E Mb with native His93 c... -

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Basic information

Entry
Database: PDB / ID: 4pq6
TitleA sperm whale myoglobin single mutant L29E Mb with native His93 coordination
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Structural Genomics / Enzyme Function Initiative / Alpha Helix bundle / Nitrite 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: 1.45 Å
AuthorsYing-Wu, L. / Xiang-shi, T. / Wei, L.
CitationJournal: ChemistryOpen / Year: 2015
Title: Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network.
Authors: Du, J.F. / Li, W. / Li, L. / Wen, G.B. / Lin, Y.W. / Tan, X.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Sep 20, 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_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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9992
Polymers17,3821
Non-polymers6161
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.866, 48.640, 78.694
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: 17382.104 Da / Num. of mol.: 1 / Mutation: L29E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185, nitrite reductase (NO-forming)
#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.: 226 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.17 %
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, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 9, 2013
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 52132 / Num. obs: 27042 / % possible obs: 51.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rsym value: 0.411
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.45-1.48199.9
1.48-1.5199.8
1.5-1.53199.5
1.53-1.56199.9
1.56-1.6199.6
1.6-1.63199.8
1.63-1.67199.6
1.67-1.72199.6
1.72-1.77199.9
1.77-1.83199.6
1.83-1.89199.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IT8

4it8


Resolution: 1.45→30.591 Å / SU ML: 0.31 / σ(F): 0.17 / Phase error: 18.54 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2069 1999 7.39 %
Rwork0.1839 --
obs0.1856 27042 97.13 %
all-52123 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.566 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3441 Å2-0 Å20 Å2
2---4.19 Å2-0 Å2
3---4.5341 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 43 226 1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061295
X-RAY DIFFRACTIONf_angle_d1.0151754
X-RAY DIFFRACTIONf_dihedral_angle_d15.596470
X-RAY DIFFRACTIONf_chiral_restr0.068181
X-RAY DIFFRACTIONf_plane_restr0.004217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4504-1.48660.23141330.2141664X-RAY DIFFRACTION91
1.4866-1.52680.20121380.21731X-RAY DIFFRACTION95
1.5268-1.57170.22931360.17811699X-RAY DIFFRACTION95
1.5717-1.62250.21731380.1891734X-RAY DIFFRACTION96
1.6225-1.68050.20881400.18411745X-RAY DIFFRACTION95
1.6805-1.74770.20391410.17691771X-RAY DIFFRACTION97
1.7477-1.82730.2221400.17311755X-RAY DIFFRACTION97
1.8273-1.92360.20621410.17231778X-RAY DIFFRACTION98
1.9236-2.04410.19511440.16791808X-RAY DIFFRACTION99
2.0441-2.20190.20461470.16331833X-RAY DIFFRACTION99
2.2019-2.42340.20321450.17751829X-RAY DIFFRACTION99
2.4234-2.77380.21451480.18841847X-RAY DIFFRACTION99
2.7738-3.49390.19791510.18071883X-RAY DIFFRACTION99
3.4939-30.59770.20661570.19891966X-RAY DIFFRACTION99

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