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- PDB-1y5k: T-To-T(High) quaternary transitions in human hemoglobin: betaD99A... -

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Basic information

Entry
Database: PDB / ID: 1y5k
TitleT-To-T(High) quaternary transitions in human hemoglobin: betaD99A deoxy low-salt (10 test sets)
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsTRANSPORT PROTEIN / HEMOGLOBIN MUTANT / GLOBIN
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / 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 / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / 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 / iron ion binding / inflammatory response / 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 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: 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_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_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

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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)64,5238
Polymers62,0574
Non-polymers2,4664
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-107 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.460, 99.880, 66.000
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: 15878.255 Da / Num. of mol.: 2 / Mutation: V1M, D99A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: 10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2004 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 26819 / % possible obs: 80.3 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2292 / % possible all: 35.1

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Processing

Software
NameVersionClassification
CRYSTALCLEARdata collection
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
REFMAC5refinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0W

1y0w


Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.663 / SU ML: 0.256 / Cross valid method: THROUGHOUT and local R-free / σ(F): 0 / ESU R: 0.465 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22655 2498 10 %10 SETS MATCHED to PDB ENTRY 1Y0W
Rwork0.16122 ---
obs0.16783 22469 75.64 %-
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: 29 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--2.53 Å20 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 172 175 4727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224724
X-RAY DIFFRACTIONr_bond_other_d0.0010.024184
X-RAY DIFFRACTIONr_angle_refined_deg2.0562.0576438
X-RAY DIFFRACTIONr_angle_other_deg1.27139710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0763570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08215762
X-RAY DIFFRACTIONr_chiral_restr0.1140.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025184
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02894
X-RAY DIFFRACTIONr_nbd_refined0.2640.31219
X-RAY DIFFRACTIONr_nbd_other0.2160.33863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.5202
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.270.56
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.321
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.57
X-RAY DIFFRACTIONr_mcbond_it0.9361.52858
X-RAY DIFFRACTIONr_mcangle_it1.74524566
X-RAY DIFFRACTIONr_scbond_it2.71231866
X-RAY DIFFRACTIONr_scangle_it4.4224.51872
LS refinement shellResolution: 2.2→2.367 Å / Total num. of bins used: 7 /
RfactorNum. reflection
Rfree0.288 183
Rwork0.204 1621

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