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- PDB-5c6y: A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-hem... -

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Basic information

Entry
Database: PDB / ID: 5c6y
TitleA sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-heme cross-link
ComponentsMyoglobin
KeywordsMETAL BINDING PROTEIN / myoglobin / METAL BINDING PROTEIN (FE)
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 / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / 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: 1.793 Å
AuthorsYuan, H. / Lin, Y.W. / Tan, X.S.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation of China31370812 China
National Science Foundation of China31270869 China
National Science Foundation of China11275090 China
Hunan Provincial Natural Science Foundation2015JJ1012 China
CitationJournal: Dalton Trans / Year: 2015
Title: How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin
Authors: Yan, D.J. / Yuan, H. / Li, W. / Xiang, Y. / He, B. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X.S.
History
DepositionJun 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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)18,0242
Polymers17,4071
Non-polymers6161
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-20 kcal/mol
Surface area7650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.062, 48.348, 79.141
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: 17407.137 Da / Num. of mol.: 1 / Mutation: L29H/F43Y
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.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.13 %
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
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.988 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.793→50 Å / Num. obs: 14678 / % possible obs: 99.7 % / Redundancy: 13 % / Net I/σ(I): 19.8
Reflection shellResolution: 1.793→1.83 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 12.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QAU

4qau


Resolution: 1.793→41.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.724 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18083 745 5.1 %RANDOM
Rwork0.15677 ---
obs0.15796 13889 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.367 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å2-0 Å2
2--0.18 Å20 Å2
3---0.99 Å2
Refinement stepCycle: 1 / Resolution: 1.793→41.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 43 161 1417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191285
X-RAY DIFFRACTIONr_bond_other_d0.0020.021254
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.9931738
X-RAY DIFFRACTIONr_angle_other_deg1.48232885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0475151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.53523.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6515230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.185154
X-RAY DIFFRACTIONr_chiral_restr0.1850.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02300
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_it2.0951.77608
X-RAY DIFFRACTIONr_mcbond_other2.0261.766607
X-RAY DIFFRACTIONr_mcangle_it2.842.638757
X-RAY DIFFRACTIONr_mcangle_other2.8432.643758
X-RAY DIFFRACTIONr_scbond_it4.2042.309677
X-RAY DIFFRACTIONr_scbond_other4.2082.309675
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3513.221981
X-RAY DIFFRACTIONr_long_range_B_refined7.93716.9911684
X-RAY DIFFRACTIONr_long_range_B_other7.70716.0511602
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.155 45 -
Rwork0.142 734 -
obs--71.08 %

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