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- PDB-3s66: Structures and oxygen affinities of crystalline human hemoglobin ... -

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Basic information

Entry
Database: PDB / ID: 3s66
TitleStructures and oxygen affinities of crystalline human hemoglobin C (beta6 Lys) in the R quaternary structures
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / hemoglobin / allostery
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 / carbon dioxide transport / response to hydrogen peroxide / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsShibayama, N. / Sugiyama, K. / Park, S.Y.
CitationJournal: To be Published
Title: Structures and oxygen affinities of crystalline human hemoglobin C (beta6 Glu->Lys) in the R and R2 quaternary structure
Authors: Shibayama, N. / Park, S.Y. / Sugiyama, K.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3306
Polymers31,0412
Non-polymers1,2894
Water3,747208
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65912
Polymers62,0814
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area6300 Å2
ΔGint-29 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.097, 53.097, 191.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 15150.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Hemoglobin C beta subunit / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15890.265 Da / Num. of mol.: 1 / Mutation: E6K
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293 K / pH: 7.2
Details: 1.65M phosphate buffer (0.528M NaH2PO4, 1.122M K2HPO4, pH 7.2), 10% (v/v) glycerol, 0.1% (w/v) D,L-homocysteine, Batch, temperature 293K

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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 210 / Detector: CCD / Date: Nov 8, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 54017 / Num. obs: 54017 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 18
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.213 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M9P

1m9p


Resolution: 1.401→18.773 Å / SU ML: 0.18 / σ(F): 0.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 2743 5.08 %RANDOM
Rwork0.2084 ---
all0.2097 53986 --
obs0.2097 53986 97.99 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.589 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 23.3344 Å2
Baniso -1Baniso -2Baniso -3
1-0.0431 Å20 Å20 Å2
2--0.0431 Å2-0 Å2
3----0.0863 Å2
Refinement stepCycle: LAST / Resolution: 1.401→18.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 90 208 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072329
X-RAY DIFFRACTIONf_angle_d1.0793190
X-RAY DIFFRACTIONf_dihedral_angle_d14.92790
X-RAY DIFFRACTIONf_chiral_restr0.069348
X-RAY DIFFRACTIONf_plane_restr0.006397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4007-1.45080.28972480.25644694X-RAY DIFFRACTION92
1.4508-1.50880.2622780.22495027X-RAY DIFFRACTION98
1.5088-1.57750.23292540.20315088X-RAY DIFFRACTION99
1.5775-1.66060.23142780.19915122X-RAY DIFFRACTION99
1.6606-1.76450.21392800.19315116X-RAY DIFFRACTION99
1.7645-1.90070.24092820.20095168X-RAY DIFFRACTION100
1.9007-2.09170.24722540.20525209X-RAY DIFFRACTION100
2.0917-2.39390.23952920.20215229X-RAY DIFFRACTION100
2.3939-3.0140.24082930.21465270X-RAY DIFFRACTION99
3.014-18.77430.21642840.20865320X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.04650.03980.10991.80.14630.99720.12960.14230.0844-0.0416-0.15030.0363-0.04320.039900.05970.01030.00630.1444-0.03310.0723-17.985334.6633-15.699
21.2202-0.5924-0.2232.04970.09081.7066-0.0280.0673-0.32860.1981-0.04940.19370.5265-0.019-0.00810.1909-0.00690.00060.0335-0.06550.1193-20.320412.6595-7.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:139))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:146))

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