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- PDB-7cez: An x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive... -

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Basic information

Entry
Database: PDB / ID: 7cez
TitleAn x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive charge
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / SPERM WHALE / MYOGLOBIN
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsYuan, H. / Lin, Y.W.
CitationJournal: To Be Published
Title: An x-ray structure of G5K/Q8K/A19K/V21K Mb mutant with a positive charge
Authors: Yuan, H. / Lin, Y.W.
History
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,1442
Polymers17,5271
Non-polymers6161
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-20 kcal/mol
Surface area8060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.372, 60.938, 63.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin


Mass: 17527.477 Da / Num. of mol.: 1 / Mutation: G5K,Q8K,A19K,V21K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (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.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 8000, 0.2 M magnesium chloride,0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 22117 / % possible obs: 99.7 % / Redundancy: 9.4 % / Biso Wilson estimate: 13.24 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Net I/σ(I): 23.3
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 1027 / Rpim(I) all: 0.188 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KRC

6krc


Resolution: 1.57→30.47 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.4805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 1211 5.5 %
Rwork0.164 20807 -
obs0.1663 22018 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.06 Å2
Refinement stepCycle: LAST / Resolution: 1.57→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 43 261 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01761467
X-RAY DIFFRACTIONf_angle_d3.16622005
X-RAY DIFFRACTIONf_chiral_restr0.1981207
X-RAY DIFFRACTIONf_plane_restr0.013256
X-RAY DIFFRACTIONf_dihedral_angle_d21.4544574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.630.20821060.19242237X-RAY DIFFRACTION96.34
1.63-1.710.22951660.17612232X-RAY DIFFRACTION99.75
1.71-1.80.231420.17582277X-RAY DIFFRACTION99.92
1.8-1.910.2171240.16582306X-RAY DIFFRACTION99.92
1.91-2.060.20571100.16482313X-RAY DIFFRACTION99.96
2.06-2.260.20731620.16132286X-RAY DIFFRACTION100
2.26-2.590.2121180.16012340X-RAY DIFFRACTION100
2.59-3.260.21731240.16612371X-RAY DIFFRACTION100
3.26-30.470.18781590.1562445X-RAY DIFFRACTION99.77

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