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- PDB-3s65: Structures and oxygen affinities of crystalline human hemoglobin ... -

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Basic information

Entry
Database: PDB / ID: 3s65
TitleStructures and oxygen affinities of crystalline human hemoglobin C (beta6 Lys) in the R2 quaternary structures
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / hemoglobin / allostery
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid 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 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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. / Sugiyama, K. / Park, S.Y.
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 / pdbx_struct_conn_angle / 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_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
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65912
Polymers62,0814
Non-polymers2,5788
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-33 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.784, 58.748, 172.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
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.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 293 K / pH: 7.6
Details: 11% (w/v) polyethylene glycol 3350, 50mM HEPES buffer, 10% (v/v) glycerol, pH 7.6, 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 26, 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: 1.8→50 Å / Num. all: 47832 / Num. obs: 47832 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 24.6
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.601 / % possible all: 63

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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: 1.8→19.396 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 35.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 2336 5.08 %RANDOM
Rwork0.2502 ---
all0.2531 46010 --
obs0.2531 46010 83.07 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.532 Å2 / ksol: 0.426 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.7202 Å20 Å2-0 Å2
2--5.4654 Å20 Å2
3----11.1856 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 180 67 4631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114708
X-RAY DIFFRACTIONf_angle_d1.4866448
X-RAY DIFFRACTIONf_dihedral_angle_d16.9831602
X-RAY DIFFRACTIONf_chiral_restr0.081700
X-RAY DIFFRACTIONf_plane_restr0.006804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8005-1.86480.4761440.41732572X-RAY DIFFRACTION50
1.8648-1.93940.44282040.35983719X-RAY DIFFRACTION72
1.9394-2.02750.36182340.31764266X-RAY DIFFRACTION82
2.0275-2.13430.36492230.29644597X-RAY DIFFRACTION88
2.1343-2.26780.33222510.27164730X-RAY DIFFRACTION91
2.2678-2.44260.32552630.26684777X-RAY DIFFRACTION92
2.4426-2.68790.33042350.26464899X-RAY DIFFRACTION93
2.6879-3.07550.29742660.26474870X-RAY DIFFRACTION92
3.0755-3.86970.29372620.23864867X-RAY DIFFRACTION91
3.8697-19.39720.26992540.21074377X-RAY DIFFRACTION79
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)
12.18770.942.38882.11021.81328.57160.19030.9687-0.0547-0.04010.3353-0.11151.22671.98330.00010.27930.2959-0.05170.5635-0.05560.218622.9788-8.7388-36.8997
22.63080.42152.39233.42480.84957.91230.306-0.36220.38480.3425-0.46080.71810.9952-1.6622-0.00080.2479-0.27420.06870.3801-0.06860.36470.5683-7.5127-28.8628
33.09991.46433.57562.56852.735110.37350.8043-0.2182-0.11291.136-0.1071-0.10432.73431.08650.00190.79030.1988-0.08810.2545-0.03320.172323.8487-7.8106-6.5258
43.73981.07432.29893.61732.70228.1781-0.5880.05410.9086-0.50960.0370.4852-1.89860.5677-0.00060.3803-0.1658-0.13040.1648-0.01980.473720.309214.4768-14.5267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and ((resseq 1:141))
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:146))
3X-RAY DIFFRACTION3chain 'C' and ((resseq 1:141))
4X-RAY DIFFRACTION4chain 'D' and ((resseq 1:146))

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