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- PDB-1j7s: Crystal Structure of deoxy HbalphaYQ, a mutant of HbA -

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Basic information

Entry
Database: PDB / ID: 1j7s
TitleCrystal Structure of deoxy HbalphaYQ, a mutant of HbA
Components(Hemoglobin) x 2
KeywordsOXYGEN STORAGE/TRANSPORT / globin / OXYGEN STORAGE-TRANSPORT COMPLEX
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 / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / regulation of blood pressure / 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 / Resolution: 2.2 Å
AuthorsMiele, A.E. / Draghi, F. / Arcovito, A. / Bellelli, A. / Brunori, M. / Travaglini-Allocatelli, C. / Vallone, B.
CitationJournal: Biochemistry / Year: 2001
Title: Control of heme reactivity by diffusion: structural basis and functional characterization in hemoglobin mutants.
Authors: Miele, A.E. / Draghi, F. / Arcovito, A. / Bellelli, A. / Brunori, M. / Travaglini-Allocatelli, C. / Vallone, B.
History
DepositionMay 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin
B: Hemoglobin
C: Hemoglobin
D: Hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7558
Polymers62,2894
Non-polymers2,4664
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-104 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.360, 84.320, 54.000
Angle α, β, γ (deg.)90.00, 99.43, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is the heterotetramer present in the asymmetric unit

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Components

#1: Protein Hemoglobin


Mass: 15222.417 Da / Num. of mol.: 2 / Fragment: alpha chain / Mutation: V1M,L29Y,H54Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P69905
#2: Protein Hemoglobin


Mass: 15922.265 Da / Num. of mol.: 2 / Fragment: beta chain / Mutation: V1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / 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.: 254 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 6.7
Details: Ammonium sulphate, ammonium phosphate, pH 6.7, SMALL TUBES, temperature 293K
Crystal grow
*PLUS
pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystal Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
14 M11(NH4)2SO4
22 M11(NH4)H2PO4
32 M11(NH4)HPO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU30011.5418
ROTATING ANODERIGAKU RU30021.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IIC1IMAGE PLATEJul 1, 1999
RIGAKU RAXIS IV2IMAGE PLATEOct 4, 1999
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2OSMIC MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→14 Å / Num. all: 28293 / Num. obs: 28293 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.1
Reflection shellHighest resolution: 2.2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.093 / % possible all: 94.2
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 96.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.054

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→14 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.21 145 random
Rwork0.16 --
all-28293 -
obs-28293 -
Refinement stepCycle: LAST / Resolution: 2.2→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4394 0 172 254 4820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.12
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 2 / Rfactor obs: 0.194 / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.12

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