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- PDB-5ziq: Crystal structure of hexacoordinated heme protein from anhydrobio... -

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Basic information

Entry
Database: PDB / ID: 5ziq
TitleCrystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4
ComponentsGlobin protein
KeywordsOXYGEN TRANSPORT / Globin / Tardigrade / UNKNOWN FUNCTION
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
: / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin domain-containing protein
Similarity search - Component
Biological speciesRamazzottius varieornatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, J. / Fukuda, Y. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS Japan
CitationJournal: FEBS J. / Year: 2019
Title: Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus.
Authors: Kim, J. / Fukuda, Y. / Inoue, T.
History
DepositionMar 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Globin protein
B: Globin protein
C: Globin protein
D: Globin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,40018
Polymers81,0764
Non-polymers3,32514
Water11,602644
1
A: Globin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2366
Polymers20,2691
Non-polymers9675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Globin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2366
Polymers20,2691
Non-polymers9675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Globin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0444
Polymers20,2691
Non-polymers7753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Globin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8852
Polymers20,2691
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.359, 59.185, 67.521
Angle α, β, γ (deg.)115.36, 97.98, 97.43
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Globin protein


Mass: 20268.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ramazzottius varieornatus (invertebrata)
Gene: RvY_09119-1, RvY_09119.1, RvY_09119 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1D1V896
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 1.87 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 4000, ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50.01 Å / Num. obs: 91088 / % possible obs: 96.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.01
Reflection shellResolution: 1.5→1.53 Å / CC1/2: 0.838

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.113 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.19392 4443 4.9 %RANDOM
Rwork0.14682 ---
obs0.14914 86645 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.445 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0.17 Å2-0.18 Å2
2--0.13 Å2-0.09 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5131 0 219 644 5994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196062
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4122.0438341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.445690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79323.825285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.216151057
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9641545
X-RAY DIFFRACTIONr_chiral_restr0.110.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214745
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.521.6252661
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0142.433384
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0731.8873401
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.32814.93310733
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.38136062
X-RAY DIFFRACTIONr_sphericity_free26.9215161
X-RAY DIFFRACTIONr_sphericity_bonded10.58556349
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 337 -
Rwork0.189 6173 -
obs--93.97 %

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