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- PDB-5x2r: Direct Observation of Conformational Population Shifts in Hemoglo... -

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Basic information

Entry
Database: PDB / ID: 5x2r
TitleDirect Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin after Adding 10 mM phosphate pH 6.9.
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 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 / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain 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: 2.7 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)193,65824
Polymers186,24312
Non-polymers7,41512
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
Buried area11430 Å2
ΔGint-102 kcal/mol
Surface area23560 Å2
MethodPISA
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
Buried area10890 Å2
ΔGint-100 kcal/mol
Surface area24160 Å2
MethodPISA
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
Buried area11070 Å2
ΔGint-109 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.768, 55.019, 138.426
Angle α, β, γ (deg.)90.00, 103.28, 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

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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: 2.28 Å3/Da / Density % sol: 45.96 %
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: 2.7→50 Å / Num. obs: 44657 / % possible obs: 96.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 80.19 Å2 / Net I/σ(I): 12

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.7→44.91 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.837 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.444
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2162 4.84 %RANDOM
Rwork0.266 ---
obs0.268 44655 95.5 %-
Displacement parametersBiso mean: 80.2 Å2
Baniso -1Baniso -2Baniso -3
1-15.0766 Å20 Å2-9.6194 Å2
2---6.0833 Å20 Å2
3----8.9933 Å2
Refine analyzeLuzzati coordinate error obs: 0.51 Å
Refinement stepCycle: 1 / Resolution: 2.7→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13032 0 516 0 13548
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813974HARMONIC2
X-RAY DIFFRACTIONt_angle_deg119170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4368SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes258HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2166HARMONIC5
X-RAY DIFFRACTIONt_it13974HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.98
X-RAY DIFFRACTIONt_other_torsion23.04
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_contact15631SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 102 4.08 %
Rwork0.3 2401 -
all0.303 2503 -
obs--72.6 %
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)
11.23520.0723-0.84110-0.67690.9215-0.01190.05480.0292-0.00760.0071-0.0384-0.01660.04290.0047-0.06570.03520.02130.09610.0343-0.037253.6125-0.081914.0516
21.35130.5928-0.29120.83560.53920.5861-0.0353-0.11260.06060.0033-0.0130.03810.0466-0.03540.0483-0.04830.0701-0.02810.04890.0475-0.035833.8258-2.569327.9257
3-0.0106-0.25660.46371.1347-0.41420.5743-0.00090.00350.024-0.0351-0.01280.0279-0.0454-0.02080.01370.05010.0004-0.0948-0.00810.0756-0.023428.917811.0097-0.359
40.04050.96910.80051.12931.25550.531-0.00690.0216-0.0298-0.0179-0.00090.06760.05480.05340.00780.05550.03250.0105-0.01430.0261-0.064229.91-13.0787-2.6612
50.87390.0793-0.46290.4017-0.15461.30660.0041-0.0453-0.01180.0218-0.01570.0636-0.0161-0.01870.0116-0.03540.00260.08670.0460.01630.0073-5.6145-28.599452.9357
61.7868-0.1356-0.30210.86930.16990.28930.0099-0.0226-0.00110.00220-0.0103-0.01850.0658-0.0099-0.0273-0.01230.00260.05180.0016-0.069416.0705-25.011642.3473
70.4057-0.1473-0.45331.81880.5565-0.2337-0.0062-0.0035-0.0199-0.02480.02510.04420.05580.0322-0.0189-0.03410.0679-0.1483-0.1056-0.04260.1186-1.3837-46.575327.1173
80.9228-1.28280.55120.5389-0.77170.3090.02030.02820.0077-0.03170.01560.0615-0.05450.0157-0.0359-0.01230.0721-0.0392-0.08170.00040.09-8.9581-24.075721.8477
90.05120.3076-0.07081.319-0.50510.3238-0.00090.02320.067-0.0172-0.01840.0084-0.03140.00590.01930.0197-0.02340.0676-0.02060.07560.031524.97015.491670.1903
101.3184-0.140.02390.827-0.53550.49790.0149-0.0143-0.07770.0107-0.0279-0.01910.00560.01580.0130.03460.03620.0277-0.0571-0.0051-0.018627.7136-16.452480.7168
11-0.05380.19940.10120.36951.00731.1469-0.0091-0.06230.0220.01440.00690.01590.0080.01820.0023-0.034-0.00120.03330.0649-0.081-0.002613.78043.824799.9428
121.8134-0.481-0.14140-0.0381-0.0229-0.00050.0181-0.0056-0.0336-0.01270.0322-0.0018-0.03520.0132-0.0733-0.03390.03870.0165-0.01990.0607-2.7908-1.775482.7821
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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