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- PDB-4pqc: A sperm whale myoglobin single mutant F43H Mb with native His93 c... -

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Basic information

Entry
Database: PDB / ID: 4pqc
TitleA sperm whale myoglobin single mutant F43H Mb with native His93 coordination
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Structural Genomics / Enzyme Function Initiative / alpha helix bundle / nitrite reductase / native state
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-like / Globin / Globin / Globin domain profile. / 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: 1.503 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 2, 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)17,9742
Polymers17,3571
Non-polymers6161
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.808, 48.055, 77.210
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: 17357.121 Da / Num. of mol.: 1 / Mutation: 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.: 216 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→30.65 Å / Num. all: 23101 / Num. obs: 22589 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.048
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.530.484194.9
1.53-1.58194.8
1.58-1.65194.5
1.65-1.73194.1
1.73-1.83193.7
1.83-1.96193.3
1.96-2.13193.1
2.13-2.38196.5
2.38-2.82199.1
2.82-4.07198.8
4.07-50195.2

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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 / Resolution: 1.503→30.65 Å / SU ML: 0.28 / σ(F): 0.16 / Phase error: 19.56 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1997 8.84 %Random
Rwork0.1811 ---
obs0.1835 22589 93.2 %-
all-23101 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.645 Å2 / ksol: 0.401 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9817 Å20 Å20 Å2
2--0.2943 Å2-0 Å2
3---4.6874 Å2
Refinement stepCycle: LAST / Resolution: 1.503→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 43 216 1474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071293
X-RAY DIFFRACTIONf_angle_d1.1731752
X-RAY DIFFRACTIONf_dihedral_angle_d14.854482
X-RAY DIFFRACTIONf_chiral_restr0.07182
X-RAY DIFFRACTIONf_plane_restr0.005213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5032-1.54080.25281300.22021335X-RAY DIFFRACTION86
1.5408-1.58240.23441320.2051368X-RAY DIFFRACTION89
1.5824-1.6290.19291390.20091424X-RAY DIFFRACTION92
1.629-1.68160.21181400.19111450X-RAY DIFFRACTION92
1.6816-1.74170.25351350.18151388X-RAY DIFFRACTION90
1.7417-1.81140.22181390.19421429X-RAY DIFFRACTION91
1.8114-1.89380.22041380.18661425X-RAY DIFFRACTION91
1.8938-1.99370.2171370.19211423X-RAY DIFFRACTION91
1.9937-2.11850.2361430.18381463X-RAY DIFFRACTION93
2.1185-2.28210.19041470.17691504X-RAY DIFFRACTION95
2.2821-2.51160.21681500.1731551X-RAY DIFFRACTION98
2.5116-2.87480.21851530.18391582X-RAY DIFFRACTION99
2.8748-3.6210.20371550.16721603X-RAY DIFFRACTION99
3.621-30.66220.18851590.18021647X-RAY DIFFRACTION97

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