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- PDB-1i3d: HUMAN CARBONMONOXY HEMOGLOBIN BART'S (GAMMA4) -

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Basic information

Entry
Database: PDB / ID: 1i3d
TitleHUMAN CARBONMONOXY HEMOGLOBIN BART'S (GAMMA4)
ComponentsHEMOGLOBIN GAMMA CHAINS
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding / Factors involved in megakaryocyte development and platelet production ...hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / oxygen binding / Factors involved in megakaryocyte development and platelet production / heme binding / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit gamma-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKidd, R.D. / Baker, H.M. / Mathews, A.J. / Brittain, T. / Baker, E.N.
CitationJournal: Protein Sci. / Year: 2001
Title: Oligomerization and ligand binding in a homotetrameric hemoglobin: two high-resolution crystal structures of hemoglobin Bart's (gamma(4)), a marker for alpha-thalassemia.
Authors: Kidd, R.D. / Baker, H.M. / Mathews, A.J. / Brittain, T. / Baker, E.N.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: HEMOGLOBIN GAMMA CHAINS
B: HEMOGLOBIN GAMMA CHAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3526
Polymers32,0632
Non-polymers1,2894
Water5,152286
1
A: HEMOGLOBIN GAMMA CHAINS
B: HEMOGLOBIN GAMMA CHAINS
hetero molecules

A: HEMOGLOBIN GAMMA CHAINS
B: HEMOGLOBIN GAMMA CHAINS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,70312
Polymers64,1254
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)60.616, 82.837, 53.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe second globin dimer of the homotetramer is generated by the two fold axis: -x, -y+1, z.

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Components

#1: Protein HEMOGLOBIN GAMMA CHAINS


Mass: 16031.255 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBG1 / Plasmid: PRMAE389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P69891
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: acetic acid/KOH, MePEG 5000, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
20.1 MHEPES1drop
32 mMsodium dithionite1drop
40.2 Macetic acid-KOH1reservoir
521 %mPEG50001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 1998 / Details: mirror
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 27848 / Num. obs: 27848 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3 / Num. unique all: 2942 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 105161
Reflection shell
*PLUS
% possible obs: 98.5 %

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CBM

1cbm


Resolution: 1.7→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2686 10 %random
Rwork0.211 ---
all-26914 --
obs-26914 88.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.1634 Å2 / ksol: 0.310647 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20.8 Å20.87 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 90 286 2638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 445 9.8 %
Rwork0.332 4101 -
obs-4546 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2hem_xplor_parhem_xplor_top
X-RAY DIFFRACTION3cmo_xplor_parcmo_xplor_top
X-RAY DIFFRACTION4water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
LS refinement shell
*PLUS
Rfactor Rfree: 0.376 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.332

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