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- PDB-1y4p: T-To-T(high) quaternary transitions in human hemoglobin: betaW37E... -

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Basic information

Entry
Database: PDB / ID: 1y4p
TitleT-To-T(high) quaternary transitions in human hemoglobin: betaW37E 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: 1.98 Å
AuthorsKavanaugh, J.S. / Rogers, P.H. / Arnone, A.
Citation
Journal: 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.
#1: Journal: Biochemistry / Year: 1998
Title: High-Resolution Crystal Structures of Human Hemoglobin with Mutations at Tryptophan 37beta: Structural Basis for a High-Affinity T-State
Authors: Kavanaugh, J.S. / Weydert, J.A. / Rogers, P.H. / Arnone, A.
History
DepositionDec 1, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionDec 7, 2004ID: 1a0y
Revision 1.0Dec 7, 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

Downloads & links

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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)64,4978
Polymers62,0314
Non-polymers2,4664
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-107 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.700, 99.100, 66.300
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 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: 15865.167 Da / Num. of mol.: 2 / Mutation: V1M, W37E
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: 2.56 Å3/Da / Density % sol: 51.96 %
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 25, 1995 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 43340 / Num. obs: 43340 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.5
Reflection shellResolution: 1.98→2.14 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 1.4 / Num. unique all: 7440 / % possible all: 84.2

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Processing

Software
NameVersionClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
REFMAC5refinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y0W

1y0w


Resolution: 1.98→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.749 / SU ML: 0.183 / Cross valid method: THROUGHOUT and local R-free / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23132 4292 10 %10 sets matched to PDB ENTRY 1Y0W
Rwork0.19185 ---
obs0.1958 38599 95.98 %-
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: 25.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--1.18 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.98→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 172 175 4723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224716
X-RAY DIFFRACTIONr_bond_other_d00.024174
X-RAY DIFFRACTIONr_angle_refined_deg1.7382.066424
X-RAY DIFFRACTIONr_angle_other_deg1.15439694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6243570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30315764
X-RAY DIFFRACTIONr_chiral_restr0.0930.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025180
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02884
X-RAY DIFFRACTIONr_nbd_refined0.2390.31118
X-RAY DIFFRACTIONr_nbd_other0.20.33698
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.5168
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.140.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.510
X-RAY DIFFRACTIONr_mcbond_it0.7831.52858
X-RAY DIFFRACTIONr_mcangle_it1.524568
X-RAY DIFFRACTIONr_scbond_it2.39731858
X-RAY DIFFRACTIONr_scangle_it3.8684.51856
LS refinement shellResolution: 1.98→2.132 Å / Total num. of bins used: 7 /
RfactorNum. reflection
Rfree0.323 718
Rwork0.286 6510

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