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- PDB-3vre: The crystal structure of hemoglobin from woolly mammoth in the de... -

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Basic information

Entry
Database: PDB / ID: 3vre
TitleThe crystal structure of hemoglobin from woolly mammoth in the deoxy form
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
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: 2.2 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta/delta hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9048
Polymers63,4384
Non-polymers2,4664
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-98 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.640, 59.080, 62.100
Angle α, β, γ (deg.)96.72, 114.36, 113.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hemoglobin subunit alpha /


Mass: 15540.505 Da / Num. of mol.: 2
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.: 2
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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: batch / pH: 6.5
Details: Ammonium sulfate, Ammonium phosphate, pH 6.5, Batch, temperature 293K, BATCH, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 24, 2010 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.51 Å / Num. obs: 28619 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.098
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.327 / % possible all: 93.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.592 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 1454 5.1 %RANDOM
Rwork0.20302 ---
obs0.20632 27132 94.42 %-
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: 35.422 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å21.28 Å21.43 Å2
2--1.99 Å2-0.2 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 172 209 4865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214796
X-RAY DIFFRACTIONr_angle_refined_deg1.3592.0556560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1545570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89524.059202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44515758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4061516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213624
X-RAY DIFFRACTIONr_mcbond_it0.5551.52852
X-RAY DIFFRACTIONr_mcangle_it1.02124582
X-RAY DIFFRACTIONr_scbond_it1.8231944
X-RAY DIFFRACTIONr_scangle_it2.7514.51978
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 93 -
Rwork0.243 1992 -
obs--93.79 %

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