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- PDB-5hlq: X-ray crystal structure of met F43H/H64A sperm whale myoglobin -

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Basic information

Entry
Database: PDB / ID: 5hlq
TitleX-ray crystal structure of met F43H/H64A sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / 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: 1.5 Å
AuthorsYuan, H.
CitationJournal: Nitric Oxide / Year: 2016
Title: Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center
Authors: Wu, L.B. / Yuan, H. / Gao, S.Q. / You, Y. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X.
History
DepositionJan 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Nov 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)17,7752
Polymers17,1591
Non-polymers6161
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-20 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.811, 49.197, 77.459
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: 17158.855 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: F43H/H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 243 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
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 8,000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.988 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.5→30.95 Å / Num. obs: 24841 / % possible obs: 99.3 % / Redundancy: 3.8 % / Net I/σ(I): 26.05
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.077 / Mean I/σ(I) obs: 20.1 / Rsym value: 0.077 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data scaling
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ERI

5eri


Resolution: 1.5→30.95 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.935 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15991 1267 5.1 %RANDOM
Rwork0.14306 ---
obs0.14394 23574 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å20 Å2
2--0.27 Å2-0 Å2
3---0.47 Å2
Refinement stepCycle: 1 / Resolution: 1.5→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 43 243 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191284
X-RAY DIFFRACTIONr_bond_other_d0.0010.021260
X-RAY DIFFRACTIONr_angle_refined_deg2.5732.0011739
X-RAY DIFFRACTIONr_angle_other_deg1.05832905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7985152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04524.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66515234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.835154
X-RAY DIFFRACTIONr_chiral_restr0.2180.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021423
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02293
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_it1.4021.092611
X-RAY DIFFRACTIONr_mcbond_other1.371.086608
X-RAY DIFFRACTIONr_mcangle_it2.0161.637762
X-RAY DIFFRACTIONr_mcangle_other2.0171.639763
X-RAY DIFFRACTIONr_scbond_it3.6741.502673
X-RAY DIFFRACTIONr_scbond_other3.6781.503671
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4962.068977
X-RAY DIFFRACTIONr_long_range_B_refined6.9512.0391780
X-RAY DIFFRACTIONr_long_range_B_other6.51510.4961629
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 88 -
Rwork0.169 1689 -
obs--97.74 %

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