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- PDB-3vrf: The crystal structure of hemoglobin from woolly mammoth in the ca... -

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Basic information

Entry
Database: PDB / ID: 3vrf
TitleThe crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta/delta hybrid
KeywordsOXYGEN TRANSPORT / woolly mammoth hemoglobin / OXYGEN STORAGE/TRANSPORT
Function / homology
Function and homology information


haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta/delta hybrid
Similarity search - Component
Biological speciesMammuthus primigenius (woolly mammoth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNoguchi, H. / Campbell, K.L. / Ho, C. / Park, S.-Y. / Tame, J.R.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of haemoglobin from woolly mammoth in liganded and unliganded states.
Authors: Noguchi, H. / Campbell, K.L. / Ho, C. / Unzai, S. / Park, S.-Y. / Tame, J.R.H.
History
DepositionApr 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 15, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta/delta hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0086
Polymers31,7192
Non-polymers1,2894
Water4,378243
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta/delta hybrid
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta/delta hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,01612
Polymers63,4384
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)109.486, 61.790, 53.570
Angle α, β, γ (deg.)90.00, 110.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein Hemoglobin subunit alpha /


Mass: 15540.505 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammuthus primigenius (woolly mammoth) / Strain: SP1349 (KIA27805) / Gene: HBA-T2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: D3U1H8
#2: Protein Hemoglobin subunit beta/delta hybrid /


Mass: 16178.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammuthus primigenius (woolly mammoth) / Strain: SP1349 (KIA27805) / Gene: HBB/D / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: D3U1H9
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: batch / pH: 7.5
Details: Sodium/potassium phosphate, pH 7.5, BATCH, temperature 293K, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2010 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 47308 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.187 / % possible all: 83.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DN3

2dn3


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.171 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19926 2390 5.1 %RANDOM
Rwork0.17094 ---
obs0.17243 44901 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.417 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.31 Å2
2--0.85 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2242 0 90 243 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1042.0553286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1875285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32123.922102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15915381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.54159
X-RAY DIFFRACTIONr_chiral_restr0.1540.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211817
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_it1.3661.51430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.522291
X-RAY DIFFRACTIONr_scbond_it3.7923977
X-RAY DIFFRACTIONr_scangle_it5.8414.5995
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 132 -
Rwork0.175 2872 -
obs--100 %

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