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- PDB-1y01: Crystal structure of AHSP bound to Fe(II) alpha-hemoglobin -

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Basic information

Entry
Database: PDB / ID: 1y01
TitleCrystal structure of AHSP bound to Fe(II) alpha-hemoglobin
Components
  • Alpha-hemoglobin stabilizing protein
  • Hemoglobin alpha chain
KeywordsOXYGEN STORAGE/TRANSPORT / AHSP / alpha hemoglobin / stabilization of alpha hemoglobin / hemoglobin oxidation and precipitation / recognition / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin metabolic process / nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / Scavenging of heme from plasma ...hemoglobin metabolic process / nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / Scavenging of heme from plasma / endocytic vesicle lumen / erythrocyte differentiation / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / unfolded protein binding / protein folding / blood microparticle / protein stabilization / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / : / Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / Globins / Globin domain profile. ...Alpha-haemoglobin stabilising protein / AHSP superfamily / Alpha-haemoglobin stabilising protein / AHSP / : / Hemoglobin, pi / Hemoglobin, alpha-type / Globin/Protoglobin / Globins / Globin domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Globin-like / Globin / Globin / Globin-like superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CHK / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit alpha / Alpha-hemoglobin-stabilizing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsFeng, L. / Gell, D.A. / Zhou, S. / Gu, L. / Gow, A.J. / Weiss, M.J. / Mackay, J.P. / Shi, Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Molecular mechanism of AHSP-mediated stabilization of alpha-hemoglobin.
Authors: Feng, L. / Gell, D.A. / Zhou, S. / Gu, L. / Kong, Y. / Li, J. / Hu, M. / Yan, N. / Lee, C. / Rich, A.M. / Armstrong, R.S. / Lay, P.A. / Gow, A.J. / Weiss, M.J. / Mackay, J.P. / Shi, Y.
History
DepositionNov 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 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 / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-hemoglobin stabilizing protein
B: Hemoglobin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1065
Polymers27,1082
Non-polymers9983
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-36 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.630, 69.630, 140.466
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha-hemoglobin stabilizing protein / Erythroid associated factor / Erythroid differentiation related factor / AHSP


Mass: 11826.327 Da / Num. of mol.: 1 / Mutation: P30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHSP, EDRF, ERAF / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZD4
#2: Protein Hemoglobin alpha chain


Mass: 15281.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905

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Non-polymers , 4 types, 49 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-CHK / 6-[(CYCLOHEXYLACETYL)(2-HYDROXYETHYL)AMINO]-6-DEOXY-D-XYLO-HEXITOL / C-HEGA-8 / CYCLOHEXYLETHANOYL-N-HYDROXYETHYLGLUCOAMIDE


Mass: 349.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H31NO7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MES, PEG2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Ni MIRROR + Ni FILTERSINGLE WAVELENGTHMx-ray1
2Ni MIRROR + Ni FILTERMADMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 9104 / Num. obs: 8822 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.055
Reflection shellResolution: 2.8→2.9 Å / Rsym value: 0.51 / % possible all: 92

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.292 460 Random
Rwork0.273 --
all0.274 9025 -
obs0.274 8330 -
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 69 46 1790
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.87

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