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- PDB-7cen: an x-ray structure of ferric L29E Mb in complex with Mg(II) -

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Basic information

Entry
Database: PDB / ID: 7cen
Titlean x-ray structure of ferric L29E Mb in complex with Mg(II)
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / myoglobin / sperm whale
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globin domain profile. / Globin / Globin / 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: 2.35 Å
AuthorsYuan, H. / Lin, Y.W.
CitationJournal: To Be Published
Title: an x-ray structure of ferric L29E Mb in complex with Mg(II)
Authors: Yuan, H. / Lin, Y.W.
History
DepositionJun 23, 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)18,0233
Polymers17,3821
Non-polymers6412
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.609, 48.538, 77.931
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: 17382.104 Da / Num. of mol.: 1 / Mutation: L29E
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 8000, 0.1 M MES PH 6.0, 0.2 M magnesium chloride

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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: 2.35→50 Å / Num. obs: 11672 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.87 Å2 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.068 / Net I/σ(I): 11.3
Reflection shellResolution: 2.35→2.39 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 327 / Rpim(I) all: 0.208

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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: 2.35→38.97 Å / SU ML: 0.2197 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 1079 10.2 %
Rwork0.1631 9495 -
obs0.1708 10574 87.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.39 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 44 112 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01481323
X-RAY DIFFRACTIONf_angle_d2.9741798
X-RAY DIFFRACTIONf_chiral_restr0.0817189
X-RAY DIFFRACTIONf_plane_restr0.0103224
X-RAY DIFFRACTIONf_dihedral_angle_d18.6535188
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.460.2751980.1875855X-RAY DIFFRACTION63.03
2.46-2.590.30881130.20341002X-RAY DIFFRACTION73.55
2.59-2.750.35861280.20491120X-RAY DIFFRACTION83.48
2.75-2.960.2781400.21257X-RAY DIFFRACTION91.19
2.96-3.260.2721480.18121314X-RAY DIFFRACTION96.82
3.26-3.730.20471500.15321341X-RAY DIFFRACTION98.74
3.73-4.70.20781500.13431319X-RAY DIFFRACTION98.66
4.7-38.970.19111520.14261287X-RAY DIFFRACTION94.48

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