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- PDB-5x2s: Direct Observation of Conformational Population Shifts in Hemoglo... -

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Basic information

Entry
Database: PDB / ID: 5x2s
TitleDirect Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 6.5.
Components(Hemoglobin subunit ...) x 2
KeywordsTRANSPORT PROTEIN / Hemoglobin / Allostery / Allosteric proteins / Oxygen binding / Bezafibrate
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
PROTOPORPHYRIN IX CONTAINING FE / PROTOPORPHYRIN IX CONTAINING NI(II) / Chem-PEM / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.39 Å
AuthorsOhki, M. / Park, S.-Y.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Direct observation of conformational population shifts in crystalline human hemoglobin.
Authors: Shibayama, N. / Ohki, M. / Tame, J.R.H. / Park, S.Y.
History
DepositionFeb 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,02025
Polymers186,24312
Non-polymers7,77713
Water64936
1
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)64,5538
Polymers62,0814
Non-polymers2,4724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5538
Polymers62,0814
Non-polymers2,4724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Hemoglobin subunit alpha
J: Hemoglobin subunit beta
K: Hemoglobin subunit alpha
L: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9159
Polymers62,0814
Non-polymers2,8335
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.603, 54.598, 138.444
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Hemoglobin subunit ... , 2 types, 12 molecules ACEGIKBDFHJL

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


Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 49 molecules

#3: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-PEM / 2-[P-[2-P-CHLOROBENZAMIDO)ETHYL]PHENOXY]-2-METHYLPROPIONIC ACID / Bezafibrate


Mass: 361.819 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H20ClNO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.7 / Details: 17%(w/v) PEG 3350, pH 7.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 65188 / % possible obs: 98.5 % / Redundancy: 4.7 % / Biso Wilson estimate: 63.46 Å2 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.39→34.99 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.663 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.58 / SU Rfree Blow DPI: 0.304 / SU Rfree Cruickshank DPI: 0.316
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3220 4.94 %RANDOM
Rwork0.245 ---
obs0.247 65168 97.8 %-
Displacement parametersBiso mean: 78.95 Å2
Baniso -1Baniso -2Baniso -3
1-14.0753 Å20 Å2-5.6149 Å2
2---4.4758 Å20 Å2
3----9.5995 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: 1 / Resolution: 2.39→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 541 36 13609
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113999HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0919203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4374SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2169HARMONIC5
X-RAY DIFFRACTIONt_it13999HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion21.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1680SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15975SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 214 4.97 %
Rwork0.284 4095 -
all0.287 4309 -
obs--88.66 %
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)
13.4831-0.0966-2.1550.2108-0.36912.6619-0.03190.11990.1098-0.04850.0351-0.1353-0.00730.0459-0.0032-0.1356-0.01540.05770.28780.1517-0.083153.7370.199114.4067
24.68081.0699-0.59531.42430.6151.3951-0.0621-0.15320.1618-0.01690.03730.12250.1003-0.23950.0249-0.15580.0307-0.01580.26270.1588-0.146533.9037-2.968128.0502
30.6018-1.0398-0.61013.6021-1.47070.7849-0.0005-0.01760.0279-0.0975-0.00820.045-0.0871-0.0020.00870.0645-0.038-0.1444-0.01510.1472-0.010928.5410.757-0.1116
41.28252.04441.48943.02212.53461.8651-0.02190.0403-0.0654-0.00440.04340.16610.12720.1177-0.02150.11240.01160.04720.03350.0607-0.171630.2194-13.2607-2.6539
53.55091.2997-1.96920.8878-0.31831.9943-0.012-0.0975-0.04760.019-0.03120.13910.0047-0.08580.0431-0.11880.07160.12160.0840.16490.0627-5.2607-28.816153.4545
63.7854-0.8848-0.57181.71390.40261.0341-0.03490.09280.0369-0.00720.0806-0.0536-0.0380.1428-0.0457-0.1284-0.080.00250.22270.0995-0.082816.2323-25.364942.3998
71.6878-0.05550.40284.1738-0.18741.90670.01080.0353-0.0849-0.02750.0050.15160.08440.1436-0.0158-0.19920.0119-0.1517-0.1893-0.010.2605-1.4866-46.86327.3987
82.388-1.16691.20291.5926-0.24871.83580.09770.1474-0.0651-0.0503-0.0020.1635-0.1981-0.0001-0.0957-0.03760.0321-0.074-0.20410.06470.2459-9.2634-24.501422.0304
90.1982-1.20720.14773.6623-0.47650.92760.00730.09730.1688-0.1152-0.07740.042-0.0997-0.00810.0701-0.04950.00730.1026-0.1310.12080.209924.85794.781470.0043
104.8185-1.8036-0.17271.25790.0851.26120.0255-0.052-0.20680.0185-0.01640.0640.13970.158-0.00910.05960.02350.0809-0.15330.0401-0.01628.0281-16.916980.791
111.24790.4935-0.68461.58930.45562.3194-0.0513-0.26440.18180.05410.01760.1153-0.01490.07270.0337-0.13910.02160.05120.0842-0.13160.040514.01193.243399.8996
125.3031-1.63260.3750.3130.65690.8663-0.00570.1332-0.0074-0.0156-0.02410.07510.0029-0.09660.0298-0.2029-0.04810.06450.0225-0.11620.219-2.6066-2.638582.8626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }

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