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- PDB-7uvb: CRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE C... -

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Basic information

Entry
Database: PDB / ID: 7uvb
TitleCRYSTAL STRUCTURE OF CARBONMONOXY HEMOGLOBIN S (LIGANDED SICKLE CELL HEMOGLOBIN) COMPLEXED WITH GBT021601
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / metalloprotein / globulin
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
FORMYL GROUP / PROTOPORPHYRIN IX CONTAINING FE / Chem-OHF / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPartridge, J.R. / Kaya, E. / Xu, Q. / Li, Z. / Strutt, S.C. / Cathers, B.E.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Br.J.Haematol. / Year: 2023
Title: GBT021601 improves red blood cell health and the pathophysiology of sickle cell disease in a murine model.
Authors: Dufu, K. / Alt, C. / Strutt, S. / Partridge, J. / Tang, T. / Siu, V. / Liao-Zou, H. / Rademacher, P. / Williams, A.T. / Muller, C.R. / Geng, X. / Pochron, M.P. / Dang, A.N. / Cabrales, P. / ...Authors: Dufu, K. / Alt, C. / Strutt, S. / Partridge, J. / Tang, T. / Siu, V. / Liao-Zou, H. / Rademacher, P. / Williams, A.T. / Muller, C.R. / Geng, X. / Pochron, M.P. / Dang, A.N. / Cabrales, P. / Li, Z. / Oksenberg, D. / Cathers, B.E.
History
DepositionApr 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)65,38014
Polymers62,0214
Non-polymers3,35910
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12110 Å2
ΔGint-115 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.334, 58.881, 173.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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

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


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


Mass: 15860.216 Da / Num. of mol.: 2 / Mutation: E6V / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P68871

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Non-polymers , 4 types, 73 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-FOR / FORMYL GROUP


Mass: 30.026 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O
#5: Chemical ChemComp-OHF / 2-hydroxy-6-({(3S)-4-[2-(2-hydroxyethyl)pyridine-3-carbonyl]morpholin-3-yl}methoxy)benzaldehyde


Mass: 386.398 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 100 mM Hepes pH 7.4, 20 mM NaCl, 28-33% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.05→39.634 Å / Num. all: 37176 / Num. obs: 37176 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.087 / Rsym value: 0.083 / Net I/av σ(I): 7.2 / Net I/σ(I): 15.5 / Num. measured all: 402048
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.16111.3760.65875553250.4281.4431.3761.799.5
2.16-2.2911.30.8450.95691050240.260.8850.8452.999.6
2.29-2.4510.80.5211.55153347920.1650.5470.5214.499.8
2.45-2.6510.90.3232.44837544200.1010.3390.3236.899.9
2.65-2.911.20.19244605641170.0590.2010.19210.899.9
2.9-3.2410.50.1186.33943837460.0380.1240.11816.5100
3.24-3.74110.06910.13659733360.0220.0720.06929.6100
3.74-4.5810.10.04813.72875228450.0160.0510.04842.1100
4.58-6.4810.30.04414.62309122450.0140.0470.04443.7100
6.48-39.6349.50.02721.71254113260.0090.0290.02758.999.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+83 / Resolution: 2.05→39.634 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2774 1996 5.38 %
Rwork0.2153 35079 -
obs0.2186 37075 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.05 Å2 / Biso mean: 70.4344 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 2.05→39.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4373 0 278 63 4714
Biso mean--73.32 57.26 -
Num. residues----573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0503-2.10160.34721350.3099244399
2.1016-2.15840.37821430.29622455100
2.1584-2.22190.29651400.2851244999
2.2219-2.29370.32511420.2723246199
2.2937-2.37560.31731370.26442480100
2.3756-2.47070.33341450.25582482100
2.4707-2.58320.37981360.26482468100
2.5832-2.71930.27871480.25432493100
2.7193-2.88960.29611420.25042494100
2.8896-3.11270.32431400.25172522100
3.1127-3.42580.32161420.23122519100
3.4258-3.92110.24451480.1962538100
3.9211-4.93870.24371460.1772573100
4.9387-39.6340.23571520.17672702100
Refinement TLS params.Method: refined / Origin x: -16.7235 Å / Origin y: -3.0104 Å / Origin z: 21.9371 Å
111213212223313233
T0.2095 Å20.0808 Å20.0165 Å2-0.3263 Å20.0074 Å2--0.3673 Å2
L1.6333 °2-0.1494 °20.0275 °2-4.0463 °2-3.8749 °2--8.1826 °2
S0.014 Å °0.0857 Å °0.1803 Å °-0.2821 Å °-0.2753 Å °-0.4659 Å °0.2988 Å °0.5858 Å °0.0705 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 143
2X-RAY DIFFRACTION1allB1 - 148
3X-RAY DIFFRACTION1allC1 - 143
4X-RAY DIFFRACTION1allC201 - 301
5X-RAY DIFFRACTION1allD2 - 148
6X-RAY DIFFRACTION1allS3 - 113

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