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- PDB-1yie: T-to-thigh quaternary transitions in human hemoglobin: betaW37A o... -

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Basic information

Entry
Database: PDB / ID: 1yie
TitleT-to-thigh quaternary transitions in human hemoglobin: betaW37A oxy (2.2MM IHP, 13% PEG) (1 test set)
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN MUTANT / GLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / Late endosomal microautophagy / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Chaperone Mediated Autophagy / regulation of blood pressure / platelet aggregation / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / inflammatory response / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKavanaugh, J.S. / Rogers, P.H. / Arnone, A.
CitationJournal: Biochemistry / Year: 2005
Title: Crystallographic evidence for a new ensemble of ligand-induced allosteric transitions in hemoglobin: the T-to-T(high) quaternary transitions.
Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A.
History
DepositionJan 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN AN IHP MOLECULE WAS NOT ADDED TO THE MODEL SINCE NO SIGNIFICANT ELECTRON DENSITY WAS ...HETEROGEN AN IHP MOLECULE WAS NOT ADDED TO THE MODEL SINCE NO SIGNIFICANT ELECTRON DENSITY WAS FOUND AT ITS BINDING SITE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemoglobin alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,50912
Polymers61,9154
Non-polymers2,5948
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.200, 99.000, 66.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe crystallographic asymmetric unit in this entry is an alpha2beta2 tetramer. the crystallographic asymmetric unit and the biological unit are equivalent.

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Components

#1: Protein Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15807.132 Da / Num. of mol.: 2 / Mutation: V1M, W37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Description: EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM ...Description: EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE CRYSTAL WAS THEN EXPOSED TO AIR AT 198K AND DATA WAS COLLECTED AT 198K.
Crystal growTemperature: 298 K / pH: 7
Details: 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.00, batch, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Feb 16, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24954 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4549 / % possible all: 90.4

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
PROLSQrefinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0T

1y0t


Resolution: 2.4→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2076 10 %MATCHED TO PDB ENTRY 1Y0T
Rwork0.185 ---
all-24197 --
obs-22833 97.1 %-
Displacement parametersBiso mean: 27.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 0 180 75 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.01
X-RAY DIFFRACTIONp_angle_d0.0250.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0250.03
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1320.1
X-RAY DIFFRACTIONp_mcbond_it2.5182
X-RAY DIFFRACTIONp_mcangle_it3.7543
X-RAY DIFFRACTIONp_scbond_it6.2484
X-RAY DIFFRACTIONp_scangle_it8.4186
X-RAY DIFFRACTIONp_plane_restr0.0090.01
X-RAY DIFFRACTIONp_chiral_restr0.130.08
X-RAY DIFFRACTIONp_singtor_nbd0.1740.2
X-RAY DIFFRACTIONp_multtor_nbd0.1840.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1840.2
X-RAY DIFFRACTIONp_planar_tor2.45
X-RAY DIFFRACTIONp_staggered_tor21.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.525
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 2.4→2.58 Å
RfactorNum. reflection
Rfree0.309 359
Rwork0.236 -
obs-3889

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