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- PDB-5yzf: X-ray crystal structure of met K42C sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 5yzf
TitleX-ray crystal structure of met K42C sperm whale myoglobin
Componentssperm whale myoglobin
KeywordsOXYGEN TRANSPORT / myoglobin
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family profile. / Globins / Globin / Globin / Globin-like / 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: 1.77 Å
AuthorsYuan, H.
CitationJournal: J. Inorg. Biochem. / Year: 2018
Title: Formation of Cys-heme cross-link in K42C myoglobin under reductive conditions with molecular oxygen
Authors: Cheng, H.M. / Yuan, H. / Wang, X.J. / Xu, J.K. / Gao, S.Q. / Wen, G.B. / Tan, X. / Lin, Y.W.
History
DepositionDec 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sperm whale myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9572
Polymers17,3401
Non-polymers6161
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-20 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.794, 47.931, 82.705
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 sperm whale myoglobin


Mass: 17340.111 Da / Num. of mol.: 1 / Mutation: K43C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30%(w/v) Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 15228 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.054 / Rsym value: 0.117 / Net I/σ(I): 24.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.503 / Rpim(I) all: 0.228 / Rsym value: 0.501 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 101M
Resolution: 1.77→34.37 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.27 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20255 760 5 %RANDOM
Rwork0.15845 ---
obs0.16066 14420 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.425 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2--0.02 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.77→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 43 202 1467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191300
X-RAY DIFFRACTIONr_bond_other_d0.0020.021270
X-RAY DIFFRACTIONr_angle_refined_deg1.822.0011762
X-RAY DIFFRACTIONr_angle_other_deg0.90532927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0485153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86124.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36915236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.108154
X-RAY DIFFRACTIONr_chiral_restr0.1530.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021441
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02299
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_it1.881.862615
X-RAY DIFFRACTIONr_mcbond_other1.8761.862614
X-RAY DIFFRACTIONr_mcangle_it2.6042.788767
X-RAY DIFFRACTIONr_mcangle_other2.6032.787768
X-RAY DIFFRACTIONr_scbond_it3.5592.246685
X-RAY DIFFRACTIONr_scbond_other3.5632.248683
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1513.184995
X-RAY DIFFRACTIONr_long_range_B_refined6.69417.3361774
X-RAY DIFFRACTIONr_long_range_B_other6.41616.2341652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.772→1.817 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 56 -
Rwork0.22 1012 -
obs--98.61 %

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