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- PDB-4n7p: Capturing the haemoglobin allosteric transition in a single cryst... -

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Basic information

Entry
Database: PDB / ID: 4n7p
TitleCapturing the haemoglobin allosteric transition in a single crystal form; Crystal structure of half-liganded human haemoglobin without phosphate at 2.8 A resolution.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsTRANSPORT PROTEIN / hybrid haemoglobin / allosteric pathway
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / 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 / Late endosomal microautophagy / Heme signaling / response to hydrogen peroxide / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PROTOPORPHYRIN IX CONTAINING NI(II) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.809 Å
AuthorsSugiyama, K. / Shibayama, N. / Park, S.Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Capturing the hemoglobin allosteric transition in a single crystal form
Authors: Shibayama, N. / Sugiyama, K. / Tame, J.R. / Park, S.Y.
History
DepositionOct 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_nat / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,65824
Polymers186,24312
Non-polymers7,41512
Water0
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5538
Polymers62,0814
Non-polymers2,4724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5538
Polymers62,0814
Non-polymers2,4724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5538
Polymers62,0814
Non-polymers2,4724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.331, 55.531, 139.681
Angle α, β, γ (deg.)90.000, 103.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 6 / Fragment: UNP residues 2-142 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 6 / Fragment: UNP residues 2-147 / Source method: isolated from a natural source / Details: blood / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32N4NiO4 / Details: blood
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Details: blood

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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: 2.32 Å3/Da / Density % sol: 46.88 % / Mosaicity: 0.329 °
Crystal growTemperature: 298 K / Method: microbatch under paraffin oil / pH: 7.6
Details: pH 7.6, microbatch under paraffin oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 5, 2010 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5 % / Number: 204553 / Rmerge(I) obs: 0.058 / Χ2: 2.27 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 41293 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.595090.310.0363.2684.2
6.037.5999.910.0423.4614.7
5.276.0399.810.0473.5824.8
4.795.2710010.0473.4664.9
4.444.7999.910.0493.2984.9
4.184.4410010.0533.4115
3.974.1899.910.0583.1915.1
3.83.9710010.0642.9725.1
3.653.810010.0712.6455.2
3.533.6510010.0822.2315.2
3.423.5310010.12.0015.3
3.323.4210010.1131.7895.3
3.233.3210010.1371.5325.3
3.153.2310010.1621.4065.3
3.083.1510010.1981.3075.2
3.023.0899.510.2091.1775.1
2.963.0298.610.2431.1344.9
2.92.9695.310.2641.1314.7
2.852.989.910.291.0824.5
2.82.858310.3021.144.4
ReflectionResolution: 2.8→50 Å / Num. all: 41293 / Num. obs: 41293 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.3
Reflection shellResolution: 2.8→2.85 Å / Rmerge(I) obs: 0.302 / % possible all: 83

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.809→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2867 2032 4.8 %
Rwork0.259 --
obs-41199 97.7 %
Solvent computationBsol: 75.3811 Å2
Displacement parametersBiso max: 149.13 Å2 / Biso mean: 92.2965 Å2 / Biso min: 31.78 Å2
Baniso -1Baniso -2Baniso -3
1--22.9 Å20 Å26.604 Å2
2--2.508 Å20 Å2
3---20.392 Å2
Refinement stepCycle: LAST / Resolution: 2.809→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13140 0 516 0 13656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.472
X-RAY DIFFRACTIONf_mcbond_it1.3521.5
X-RAY DIFFRACTIONf_scbond_it1.682
X-RAY DIFFRACTIONf_mcangle_it2.3552
X-RAY DIFFRACTIONf_scangle_it2.6542.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:dna-rna.param
X-RAY DIFFRACTION5PARAM:hem.par

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