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- PDB-5b84: X-ray crystal structure of met I107Y sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 5b84
TitleX-ray crystal structure of met I107Y sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE
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: 1.61 Å
AuthorsYuan, H.
CitationJournal: Mol Biosyst / Year: 2016
Title: Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin
Authors: Liao, F. / Yuan, H. / Du, K.J. / You, Y. / Gao, S.Q. / Wen, G.B. / Lin, Y.W. / Tan, X.
History
DepositionJun 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Nov 8, 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9012
Polymers17,2851
Non-polymers6161
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.911, 48.560, 78.184
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: 17284.969 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: I107Y
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.: 217 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30%(w/v) Polyethylene glycol 8,000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 19658 / % possible obs: 96.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 34.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.8 % / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
PHENIXmodel building
MOLREPphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QAU

4qau


Resolution: 1.61→35.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.713 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19418 1002 5.1 %RANDOM
Rwork0.16594 ---
obs0.16743 18623 96.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.091 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0 Å20 Å2
2--0.35 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.61→35.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 43 217 1480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191312
X-RAY DIFFRACTIONr_bond_other_d0.0010.021276
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.9961779
X-RAY DIFFRACTIONr_angle_other_deg0.92532941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6995155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39824.28656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.069154
X-RAY DIFFRACTIONr_chiral_restr0.1570.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021465
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02307
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8832.197620
X-RAY DIFFRACTIONr_mcbond_other1.8492.196617
X-RAY DIFFRACTIONr_mcangle_it2.5653.293775
X-RAY DIFFRACTIONr_mcangle_other2.5643.295776
X-RAY DIFFRACTIONr_scbond_it3.6292.637692
X-RAY DIFFRACTIONr_scbond_other3.6322.638690
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2563.7841004
X-RAY DIFFRACTIONr_long_range_B_refined6.63120.4631788
X-RAY DIFFRACTIONr_long_range_B_other6.32819.3471674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.608→1.649 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 67 -
Rwork0.193 1294 -
obs--92.59 %

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