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- PDB-3hyu: Crystal structure of the altitude adapted hemoglobin of guinea pig. -

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Basic information

Entry
Database: PDB / ID: 3hyu
TitleCrystal structure of the altitude adapted hemoglobin of guinea pig.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Altitude Adaptation / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / heme binding / metal ion binding
Similarity search - Function
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 / PHOSPHATE ION / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsPairet, B. / Jaenicke, E.
CitationJournal: Plos One / Year: 2010
Title: Structure of the altitude adapted hemoglobin of guinea pig in the R2-state.
Authors: Pairet, B. / Jaenicke, E.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Feb 18, 2015Group: Other
Revision 1.4Sep 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8138
Polymers31,2002
Non-polymers1,6136
Water4,125229
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,62516
Polymers62,3994
Non-polymers3,22612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Surface area2 Å2
Unit cell
Length a, b, c (Å)83.540, 89.950, 82.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemoglobin subunit alpha / Hemoglobin alpha chain / Alpha-globin


Mass: 15253.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Blood / Source: (natural) Cavia porcellus (domestic guinea pig) / Strain: Dunkin Hartley / References: UniProt: P01947
#2: Protein Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 15946.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cavia porcellus (domestic guinea pig) / References: UniProt: P02095
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: Sodium Phosphate, Ammonia Sulfate, pH 6.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 6, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionNumber: 472680 / Rmerge(I) obs: 0.052 / D res high: 1.67 Å / Num. obs: 36377 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
7.4619.5940486.310.039
5.277.4679610010.047
4.35.27100399.910.046
3.734.3118899.910.039
3.333.73132210010.037
3.043.33145610010.04
2.823.04157910010.042
2.642.82169110010.046
2.492.64180010010.048
2.362.49187810010.053
2.252.36199110010.055
2.152.25207710010.058
2.072.15216310010.065
1.992.07224110010.072
1.921.99231299.910.083
1.861.92238810010.098
1.811.86246310010.113
1.761.81254410010.133
1.711.76261510010.166
1.671.7124669210.255
ReflectionResolution: 1.67→19.59 Å / Num. all: 36376 / Num. obs: 36376 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.501 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.8
Reflection shellResolution: 1.67→1.71 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 9.95 / Num. measured obs: 17763 / Num. unique all: 2466 / Num. unique obs: 2466 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.09 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.59 Å
Translation2.5 Å19.59 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D5X

2d5x


Resolution: 1.67→19.59 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.893 / SU B: 1.459 / SU ML: 0.051 / SU R Cruickshank DPI: 0.097 / SU Rfree: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1822 5 %RANDOM
Rwork0.177 ---
all0.179 36376 --
obs0.179 36376 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.02 Å2 / Biso mean: 12.375 Å2 / Biso min: 3.82 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.67→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 106 229 2537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212375
X-RAY DIFFRACTIONr_angle_refined_deg1.1652.0563252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4855285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44423.66790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14415365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.518156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211766
X-RAY DIFFRACTIONr_mcbond_it0.6841.51426
X-RAY DIFFRACTIONr_mcangle_it1.34422285
X-RAY DIFFRACTIONr_scbond_it2.2413949
X-RAY DIFFRACTIONr_scangle_it3.5444.5967
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 112 -
Rwork0.304 2335 -
all-2447 -
obs-2466 92.13 %

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