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- PDB-4pqb: A sperm whale myoglobin double mutant L29E/F43H Mb with a non-nat... -

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Basic information

Entry
Database: PDB / ID: 4pqb
TitleA sperm whale myoglobin double mutant L29E/F43H Mb with a non-native bis-His (His64/His93) coordination
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Structural Genomics / Enzyme Function Initiative / Alpha helix bundle
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: 1.942 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
DepositionMar 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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)17,9902
Polymers17,3731
Non-polymers6161
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.968, 60.898, 75.356
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: 17373.078 Da / Num. of mol.: 1 / Fragment: Whale sperm mutant / Mutation: L29E/F43H
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
#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.: 148 / 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
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.94→47.36 Å / Num. all: 12082 / Num. obs: 11952 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.1 / Rsym value: 0.089

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
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: 1.942→47.36 Å / SU ML: 0.42 / σ(F): 1.38 / Phase error: 19.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1196 10.01 %RANDOM
Rwork0.1817 ---
obs0.1855 11952 98.96 %-
all-12082 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.376 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8922 Å20 Å20 Å2
2--1.2643 Å2-0 Å2
3---0.7268 Å2
Refinement stepCycle: LAST / Resolution: 1.942→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 43 148 1407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091294
X-RAY DIFFRACTIONf_angle_d1.1691753
X-RAY DIFFRACTIONf_dihedral_angle_d16.23483
X-RAY DIFFRACTIONf_chiral_restr0.069181
X-RAY DIFFRACTIONf_plane_restr0.004214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9424-2.02010.2631220.18981098X-RAY DIFFRACTION93
2.0201-2.11210.23161310.18331174X-RAY DIFFRACTION98
2.1121-2.22340.20181290.18351161X-RAY DIFFRACTION100
2.2234-2.36270.23221310.1741188X-RAY DIFFRACTION100
2.3627-2.54520.21651330.1871194X-RAY DIFFRACTION100
2.5452-2.80130.22621330.19741198X-RAY DIFFRACTION100
2.8013-3.20650.23921350.19051215X-RAY DIFFRACTION100
3.2065-4.03960.18331360.16651223X-RAY DIFFRACTION100
4.0396-47.37880.22671460.1811305X-RAY DIFFRACTION100

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