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- PDB-5x2u: Direct Observation of Conformational Population Shifts in Hemoglo... -

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Basic information

Entry
Database: PDB / ID: 5x2u
TitleDirect Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 80 mM phosphate pH 6.7.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
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) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.53 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 1.1Feb 21, 2018Group: 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)193,65824
Polymers186,24312
Non-polymers7,41512
Water0
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
Water0
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
Water0
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)64,5538
Polymers62,0814
Non-polymers2,4724
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.886, 55.812, 139.963
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#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

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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: 2.34 Å3/Da / Density % sol: 47.53 %
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: 2.53→50 Å / Num. obs: 57084 / % possible obs: 98.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 61.52 Å2 / Net I/σ(I): 15.3

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.53→39.74 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.275 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.908 / SU Rfree Blow DPI: 0.326 / SU Rfree Cruickshank DPI: 0.34
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2891 5.07 %RANDOM
Rwork0.231 ---
obs0.233 57071 97.8 %-
Displacement parametersBiso mean: 68.23 Å2
Baniso -1Baniso -2Baniso -3
1-10.098 Å20 Å2-3.8907 Å2
2---6.8515 Å20 Å2
3----3.2464 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.53→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 516 0 13548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113973HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0419167HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4367SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2165HARMONIC5
X-RAY DIFFRACTIONt_it13973HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion20.15
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_contact15576SEMIHARMONIC4
LS refinement shellResolution: 2.53→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 164 4.66 %
Rwork0.281 3354 -
all0.283 3518 -
obs--82.39 %
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)
13.99230.1257-2.290.01610.51470.9617-0.06040.15670.1292-0.00850.0356-0.07190.04060.21550.0248-0.12270.0221-0.01130.20350.0968-0.073454.409532.706314.016
24.7575-0.02840.58730.7182-0.25782.9364-0.0957-0.33340.0962-0.072-0.06120.07360.13680.02750.1569-0.04340.04870.0106-0.0999-0.0329-0.021334.916331.269628.428
3-0.07-0.4584-0.08931.4355-0.1642.2637-0.01020.10120.0966-0.0085-0.13410.0142-0.09160.04140.1443-0.0431-0.0533-0.1210.06090.12070.009528.090542.6886-0.4762
40.35250.77862.06881.82031.27813.27080.02380.1278-0.0748-0.0428-0.03630.08810.19720.05210.01250.035-0.02310.08340.0706-0.148-0.100130.230618.2692-0.7299
52.82150.1222-2.41560-0.44541.5370.014-0.1581-0.00740.041-0.05070.18250.0047-0.09070.0367-0.0657-0.10820.13980.1664-0.1704-0.0149-4.41134.988854.0081
62.88770.15940.17893.03620.89431.95970.0635-0.22860.0731-0.060.0321-0.0236-0.06420.1149-0.0956-0.0301-0.03550.0637-0.0634-0.0242-0.052117.3378.462943.4288
72.88330.2002-0.51581.72730.66251.38510.01050.0412-0.10420.0517-0.0937-0.00170.1162-0.1590.0832-0.08010.0097-0.1345-0.1222-0.04480.1718-0.2658-13.390328.4626
82.9355-1.5221.39741.8434-1.00020.6310.00590.06740.1377-0.0758-0.04720.0949-0.0966-0.03180.0413-0.0890.1568-0.1573-0.056-0.04580.1551-7.74929.10822.6435
91.12541.2916-0.57082.6205-0.76430.72560.0170.09270.10230.00050.0464-0.0596-0.06040.0294-0.0634-0.0313-0.00880.09140.01950.12190.017525.782339.791371.9394
103.3283-1.04390.67380.5328-1.79751.096-0.00510.0127-0.10620.1068-0.0195-0.10310.04720.03210.02450.04250.0197-0.0773-0.0772-0.0425-0.022228.530117.493181.995
110.67961.12420.056201.22472.5142-0.0218-0.13780.05130.07570.0334-0.00650.02520.0038-0.0115-0.12970.02790.01590.1358-0.1102-0.007114.162437.3229101.1791
124.0031-1.1075-0.36350.61110.35350.07170.00440.0453-0.0229-0.0549-0.0290.03960.0136-0.06720.0246-0.1289-0.02930.09070.05750.00920.0463-2.036532.023183.4898
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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