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- PDB-3d17: A triply ligated crystal structure of relaxed state human hemoglobin -

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Basic information

Entry
Database: PDB / ID: 3d17
TitleA triply ligated crystal structure of relaxed state human hemoglobin
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN BINDING / liganded / relaxed / triply ligated / ligand uptake / ligand channel / Acetylation / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Oxygen transport / Polymorphism / Transport / Hypotensive agent / Pyruvate / S-nitrosylation / Vasoactive
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / 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 / 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 / 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 / ficolin-1-rich granule lumen / blood microparticle / 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / TOLUENE / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSafo, M.K. / Musayev, F.N. / Jenkins, J. / Abraham, D.J.
CitationJournal: TO BE PUBLISHED
Title: A triply ligated crystal structure of relaxed state human hemoglobin
Authors: Jenkins, J. / Musayev, F.N. / Abraham, D.J. / Safo, M.K.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,00815
Polymers62,0814
Non-polymers2,92711
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12890 Å2
ΔGint-115.3 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.282, 87.282, 174.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

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


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Red blood cell / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Hemoglobin beta chain / Beta-globin


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: Red blood cell / References: UniProt: P68871

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Non-polymers , 5 types, 99 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8
#5: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.4
Details: NaPhosph, KPhosph, Toluene, pH 6.4, liquid diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→39 Å / Num. obs: 16653 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 7.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1633 / % possible all: 95.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.429 / Cor.coef. Fo:Fc: 0.462 / Cor.coef. Io to Ic: 0.484
Highest resolutionLowest resolution
Rotation4 Å8 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IJW

1ijw


Resolution: 2.8→19.9 Å / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 807 -random
Rwork0.232 ---
all0.27 16589 --
obs0.255 16148 93.5 %-
Displacement parametersBiso mean: 42.686 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2--3.06 Å20 Å2
3----6.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 198 90 4672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d1.42
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 3.2
RfactorNum. reflection% reflection
Rfree0.377 138 -
Rwork0.35 --
obs-2590 92 %

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