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- PDB-8pur: DexyHemoglobin structure from serial synchrotron crystallography ... -

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Basic information

Entry
Database: PDB / ID: 8pur
TitleDexyHemoglobin structure from serial synchrotron crystallography with fixed target
Components
  • Hemoglobin subunit beta
  • Hemoglobin, alpha 1
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 / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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, alpha 1
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3884
Polymers31,1552
Non-polymers1,2332
Water1,26170
1
A: Hemoglobin, alpha 1
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin, alpha 1
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7758
Polymers62,3094
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11480 Å2
ΔGint-109 kcal/mol
Surface area23570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.290, 63.060, 54.750
Angle α, β, γ (deg.)90.000, 111.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hemoglobin, alpha 1


Mass: 15122.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: A0A3Q2H875
#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.: 70 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
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: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→53.504 Å / Num. obs: 29515 / % possible obs: 100 % / Redundancy: 205 % / CC1/2: 0.9914 / Net I/σ(I): 12.48
Reflection shellResolution: 1.85→1.916 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1461 / CC1/2: 0.9049

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→53.504 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.985 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.161 / SU B: 2.697 / SU ML: 0.078 / Average fsc free: 0.97 / Average fsc work: 0.9809 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.088
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1622 1474 4.994 %
Rwork0.1299 28041 -
all0.132 --
obs-29515 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: 70.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.493 Å20 Å21.674 Å2
2---1.483 Å2-0 Å2
3----0.228 Å2
Refinement stepCycle: LAST / Resolution: 1.85→53.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2190 0 86 70 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122347
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162189
X-RAY DIFFRACTIONr_angle_refined_deg2.031.7113209
X-RAY DIFFRACTIONr_angle_other_deg0.9051.6245032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.97256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56110361
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.9251094
X-RAY DIFFRACTIONr_chiral_restr0.1130.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022705
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02533
X-RAY DIFFRACTIONr_nbd_refined0.2050.2433
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1290.21758
X-RAY DIFFRACTIONr_nbtor_refined0.160.21147
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0620.21267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.212
X-RAY DIFFRACTIONr_nbd_other0.0660.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.24
X-RAY DIFFRACTIONr_mcbond_it5.3766.8291142
X-RAY DIFFRACTIONr_mcbond_other5.3656.831142
X-RAY DIFFRACTIONr_mcangle_it6.57612.2841424
X-RAY DIFFRACTIONr_mcangle_other6.57512.2921425
X-RAY DIFFRACTIONr_scbond_it8.3577.6021205
X-RAY DIFFRACTIONr_scbond_other8.3487.5971203
X-RAY DIFFRACTIONr_scangle_it11.71913.591785
X-RAY DIFFRACTIONr_scangle_other11.72213.591785
X-RAY DIFFRACTIONr_lrange_it12.38867.4032594
X-RAY DIFFRACTIONr_lrange_other12.39167.4082591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.85-1.8980.2991230.26220620.26421850.9290.9430.247
1.898-1.950.225910.21620230.21721140.9570.9640.201
1.95-2.0060.2521030.19419360.19720390.9510.9720.176
2.006-2.0680.1911030.16618820.16819850.9750.9820.153
2.068-2.1360.2141060.16318310.16619370.9710.9830.153
2.136-2.2110.199890.15117980.15318870.9770.9870.145
2.211-2.2940.211020.15417060.15718080.9740.9860.15
2.294-2.3870.204840.15216720.15517560.9750.9870.155
2.387-2.4930.206780.15315850.15616630.9760.9870.161
2.493-2.6150.195780.14715210.1515990.9790.9880.159
2.615-2.7560.189810.15814390.1615200.9760.9860.178
2.756-2.9230.226770.15813560.16114330.9720.9850.179
2.923-3.1240.239670.16513010.16913680.9660.9830.192
3.124-3.3730.185640.15411850.15612490.9750.9860.179
3.373-3.6930.156610.13811230.13911840.9860.9890.164
3.693-4.1270.122520.11310080.11310600.9890.9920.139
4.127-4.7610.134310.0969040.0989350.990.9950.121
4.761-5.8190.165300.1157630.1177930.9870.9930.152
5.819-8.1810.159340.1185960.126300.9860.9920.159
8.181-53.5040.108200.1123490.1113690.9950.990.135

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