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- PDB-8puq: MetHemoglobin structure from serial synchrotron crystallography w... -

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Basic information

Entry
Database: PDB / ID: 8puq
TitleMetHemoglobin structure from serial synchrotron crystallography with fixed target
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Horse hemoglobin / SSX / fixed target
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBjelcic, M. / Sigfridsson Clauss, K. / Aurelius, O. / Milas, M. / Nan, J. / Ursby, T.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Anaerobic fixed-target serial crystallography using sandwiched silicon nitride membranes.
Authors: Bjelcic, M. / Sigfridsson Clauss, K.G.V. / Aurelius, O. / Milas, M. / Nan, J. / Ursby, T.
History
DepositionJul 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2464
Polymers31,0132
Non-polymers1,2332
Water1,67593
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4938
Polymers62,0274
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area10800 Å2
ΔGint-108 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.530, 63.080, 54.690
Angle α, β, γ (deg.)90.000, 111.020, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14981.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P01958
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 293.15 K / Method: batch mode / pH: 7.5 / Details: 26%v PEG3350, 10mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→53.55 Å / Num. obs: 25258 / % possible obs: 100 % / Redundancy: 176 % / CC1/2: 0.9903 / R split: 0.075 / Net I/σ(I): 10.6
Reflection shellResolution: 1.95→2.02 Å / Mean I/σ(I) obs: 1.37 / Num. unique obs: 1261 / CC1/2: 0.7593 / R split: 0.4194

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→53.55 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.975 / SU B: 7.71 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.1 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1741 1211 4.795 %
Rwork0.1252 24047 -
all0.127 --
obs-25258 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.398 Å20 Å21.89 Å2
2---2.054 Å2-0 Å2
3---0.157 Å2
Refinement stepCycle: LAST / Resolution: 1.95→53.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 86 93 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122359
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162190
X-RAY DIFFRACTIONr_angle_refined_deg2.0371.7183229
X-RAY DIFFRACTIONr_angle_other_deg0.8431.6285033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.25357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41410360
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4221096
X-RAY DIFFRACTIONr_chiral_restr0.1060.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022756
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02544
X-RAY DIFFRACTIONr_nbd_refined0.2080.2470
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1420.21781
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21161
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.21316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.213
X-RAY DIFFRACTIONr_nbd_other0.1040.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.29
X-RAY DIFFRACTIONr_mcbond_it4.3735.0071145
X-RAY DIFFRACTIONr_mcbond_other4.3565.0071145
X-RAY DIFFRACTIONr_mcangle_it5.1568.991430
X-RAY DIFFRACTIONr_mcangle_other5.1548.9951431
X-RAY DIFFRACTIONr_scbond_it6.955.6761214
X-RAY DIFFRACTIONr_scbond_other6.935.6721212
X-RAY DIFFRACTIONr_scangle_it9.65410.0911798
X-RAY DIFFRACTIONr_scangle_other9.66110.091798
X-RAY DIFFRACTIONr_lrange_it10.44850.8722673
X-RAY DIFFRACTIONr_lrange_other10.44950.6092668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.287760.2691764X-RAY DIFFRACTION100
2.001-2.0550.27920.2291712X-RAY DIFFRACTION100
2.055-2.1150.206890.211684X-RAY DIFFRACTION100
2.115-2.180.218800.1831636X-RAY DIFFRACTION100
2.18-2.2510.211790.1711586X-RAY DIFFRACTION100
2.251-2.330.215740.161523X-RAY DIFFRACTION100
2.33-2.4180.186610.1431484X-RAY DIFFRACTION100
2.418-2.5160.171710.1421416X-RAY DIFFRACTION100
2.516-2.6280.199730.1351368X-RAY DIFFRACTION100
2.628-2.7560.205650.1431295X-RAY DIFFRACTION100
2.756-2.9050.2660.1491230X-RAY DIFFRACTION100
2.905-3.080.203660.1381170X-RAY DIFFRACTION100
3.08-3.2920.207620.1341108X-RAY DIFFRACTION100
3.292-3.5550.166560.1291010X-RAY DIFFRACTION100
3.555-3.8920.15550.11955X-RAY DIFFRACTION100
3.892-4.3490.117370.097869X-RAY DIFFRACTION100
4.349-5.0160.161400.092763X-RAY DIFFRACTION100
5.016-6.130.182360.119647X-RAY DIFFRACTION100
6.13-8.6130.149170.117526X-RAY DIFFRACTION100
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)
13.16190.3994-2.12632.11770.16873.5022-0.06570.1894-0.2485-0.10250.0368-0.13650.24460.14550.02890.03770.0201-0.00610.0521-0.02910.033-20.756.750113.9984
22.5271-0.53230.64062.53350.11793.3403-0.0177-0.18170.27420.08390.0194-0.1828-0.3430.1437-0.00170.0412-0.020.00050.0256-0.0220.0374-25.392524.2930.2225
Refinement TLS groupSelection: ALL

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