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- PDB-6jp1: An X-ray structure of met sperm whale F43Y/T67R myoglobin with Ty... -

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Basic information

Entry
Database: PDB / ID: 6jp1
TitleAn X-ray structure of met sperm whale F43Y/T67R myoglobin with Tyr-heme double cross-links
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 / 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: 1.99 Å
AuthorsLin, Y.W. / Yuan, H.
CitationJournal: Chem.Commun.(Camb.) / Year: 2019
Title: Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases.
Authors: Liu, C. / Yuan, H. / Liao, F. / Wei, C.W. / Du, K.J. / Gao, S.Q. / Tan, X. / Lin, Y.W.
History
DepositionMar 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4774
Polymers34,2442
Non-polymers1,2332
Water3,837213
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7382
Polymers17,1221
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7382
Polymers17,1221
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.406, 33.604, 72.886
Angle α, β, γ (deg.)90.00, 117.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 1 - 151 / Label seq-ID: 1 - 151

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Myoglobin


Mass: 17121.863 Da / Num. of mol.: 2 / Mutation: F43Y, T67R
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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate,0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 21592 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.103 / Net I/σ(I): 19.71
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 2736 / Rpim(I) all: 0.675 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VXA

1vxa


Resolution: 1.99→36.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.367 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22049 1102 5.1 %RANDOM
Rwork0.17104 ---
obs0.17349 20490 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.01 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.99→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2459 0 43 213 2715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132585
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172482
X-RAY DIFFRACTIONr_angle_refined_deg2.9911.6943494
X-RAY DIFFRACTIONr_angle_other_deg1.4641.625750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68322.712118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44115476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3681510
X-RAY DIFFRACTIONr_chiral_restr0.1520.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022829
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02535
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_it1.3031.6711208
X-RAY DIFFRACTIONr_mcbond_other1.3011.671207
X-RAY DIFFRACTIONr_mcangle_it1.992.4981509
X-RAY DIFFRACTIONr_mcangle_other1.992.51509
X-RAY DIFFRACTIONr_scbond_it2.1751.9611377
X-RAY DIFFRACTIONr_scbond_other2.1761.9621375
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4492.8031984
X-RAY DIFFRACTIONr_long_range_B_refined5.22121.2413238
X-RAY DIFFRACTIONr_long_range_B_other4.90320.3783118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4864 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 66 -
Rwork0.225 1376 -
obs--91.91 %

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