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- PDB-5x2t: Direct Observation of Conformational Population Shifts in Hemoglo... -

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Basic information

Entry
Database: PDB / ID: 5x2t
TitleDirect Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 4 mM bezafibrate pH 7.2.
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 / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / 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: 2.64 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 20, 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
Water00
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)64,9159
Polymers62,0814
Non-polymers2,8335
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)228.494, 55.024, 138.504
Angle α, β, γ (deg.)90.00, 103.38, 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


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


Mass: 361.819 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClNO4

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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: 2.27 Å3/Da / Density % sol: 45.91 %
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: 2.64→50 Å / Num. obs: 48972 / % possible obs: 98.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 72.02 Å2 / Net I/σ(I): 11.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.64→48.77 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.882 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.372
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2395 4.89 %RANDOM
Rwork0.232 ---
obs0.234 48934 97.9 %-
Displacement parametersBiso mean: 76.37 Å2
Baniso -1Baniso -2Baniso -3
1-15.2634 Å20 Å2-6.3208 Å2
2---2.4477 Å20 Å2
3----12.8157 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: 1 / Resolution: 2.64→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 541 0 13573
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114000HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0919206HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4375SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2170HARMONIC5
X-RAY DIFFRACTIONt_it14000HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion22
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_contact15952SEMIHARMONIC4
LS refinement shellResolution: 2.64→2.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 136 4.41 %
Rwork0.266 2947 -
all0.267 3083 -
obs--83.88 %
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)
12.64680.231-2.05180.03480.01621.6575-0.02420.15080.1263-0.02960.0536-0.07520.01720.047-0.0294-0.14780.02130.01570.23240.1248-0.067353.74751.226714.15
24.20060.3348-0.00931.28711.0071.2903-0.0776-0.10760.1415-0.03310.07860.03110.1278-0.1357-0.001-0.10790.0245-0.02550.10810.1485-0.093834.0175-1.640227.9481
30.5025-0.7553-0.28432.1072-0.29621.16670.00060.02210.0466-0.064-0.03270.0508-0.1132-0.00080.03220.00240.0005-0.08630.02430.1449-0.019128.781311.9069-0.3472
40.94660.66730.10821.44891.00691.3935-0.00560.0186-0.0595-0.01640.00780.15070.12080.1113-0.00220.09340.04340.0305-0.00070.0656-0.143230.1306-12.2168-2.7405
52.81551.2792-2.08360.6502-1.20131.5479-0.0169-0.078-0.02260.044-0.02340.1230.0479-0.09460.04030.00580.01790.1327-0.02060.13120.0591-5.3683-27.805653.1965
63.2439-0.7364-0.48712.44090.62641.1469-0.02870.07730.0388-0.00430.0565-0.0054-0.03850.0897-0.0278-0.0629-0.0735-0.02650.05620.0855-0.09116.1999-24.201242.2819
71.8766-0.3373-0.19263.24580.10251.27730.01020.0145-0.0703-0.0783-0.02340.15970.04570.08410.0132-0.1474-0.0064-0.1626-0.1989-0.00040.249-1.2299-45.93526.9981
81.8104-2.04010.43321.7441-1.29640.42690.06080.0541-0.0032-0.07250.01440.141-0.11010.0255-0.07520.00560.0171-0.1604-0.2132-0.01440.2158-9.1209-23.528121.7815
9-0.1678-0.99960.2283.07860.16751.7559-0.00830.07290.1513-0.07660.02670.0508-0.0412-0.0011-0.0184-0.0268-0.00790.1167-0.1260.13910.14924.49676.430870.3544
102.7423-0.12320.23760.972-0.24311.7272-0.0245-0.0305-0.10820.02180.03930.00620.11880.0481-0.01480.07330.08810.1123-0.13430.0455-0.034727.7059-15.519480.701
111.7950.9735-0.46061.48731.02591.665-0.048-0.18210.10780.06970.00130.08340.05290.11060.0467-0.09790.10180.0330.0744-0.1217-0.005813.45074.373599.89
123.2152-1.0830.29560.86930.4770.0143-0.02440.09510.0019-0.0533-0.0180.07540.0243-0.04270.0424-0.1474-0.02730.07270.0141-0.05580.1389-2.9402-1.491182.7662
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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