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- PDB-6sva: Multicrystal structure of equine Haemoglobin at room temperature ... -

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Basic information

Entry
Database: PDB / ID: 6sva
TitleMulticrystal structure of equine Haemoglobin at room temperature using a multilayer monochromator.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsTRANSPORT PROTEIN / Room temperature DMM Multilayer monochromator Multicrystal
Function / homology
Function and homology information


hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding / 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 / Globins / Globin domain profile. / Globin-like / Globin / Globin ...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 / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsSandy, J. / Sanchez-Weatherby, J. / Mikolajek, H. / Lewis, G. / Angus, R.
CitationJournal: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature crystallography at VMXi
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.G. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
History
DepositionSep 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
Water2,144119
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
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)108.515, 62.992, 54.591
Angle α, β, γ (deg.)90.000, 111.051, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.7655.43
2
3
4
5
6
7
Crystal grow
Temperature (K)Crystal-IDMethodDetailspH
2931vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350
2932vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350
2933vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350
2934vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350
2935vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350
2936vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350 0.1 M Bis Tris Propane6.5
2937vapor diffusion, sitting drop0.2 M Sodium Sulphate 20% PEG 3350 0.1 M Bis Tris Propane6.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 18, 2019
RadiationMonochromator: DMM (Double Multilayer Monochromator) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection

Biso Wilson estimate: 27.27 Å2 / Entry-ID: 6SVA / Diffraction-ID: 1 / Resolution: 1.92→50.64 Å

Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allNet I/σ(I)
2160645.61.60.9940.0470.0380.0610.2
2160644.51.80.9950.0630.0480.087.1
2160651.41.60.9880.070.0610.0926.3
2160653.71.70.9460.1620.1290.2093.1
2160643.220.9930.0760.0560.0957.3
2160646.21.80.9930.0670.0510.0856.5
2160656.61.60.9690.1020.0960.144.9
2160881.86.10.9910.1140.0430.1239.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.11-2.1110.3831.71390.6320.3830.54110.6
1.99-2.021.20.5330.91880.5750.5330.75418.7
2-2.031.10.4261.12240.7490.4260.60218.7
2.11-2.151.30.58512590.6960.5850.82726.4
2.08-2.121.20.3761.82320.840.3420.5122.4
2.01-2.041.10.54612300.1650.5460.77319.4
2.08-2.121.20.5910.912800.410.5910.83627.2
1.92-1.9510.6311290.6310.8939.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C6E

5c6e


Resolution: 1.92→50.64 Å / SU ML: 0.1467 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.4851
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1733 1035 4.79 %
Rwork0.1408 20571 -
obs0.1424 21606 81.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.59 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 43 119 2370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01832377
X-RAY DIFFRACTIONf_angle_d1.43113272
X-RAY DIFFRACTIONf_chiral_restr0.0837354
X-RAY DIFFRACTIONf_plane_restr0.0108412
X-RAY DIFFRACTIONf_dihedral_angle_d18.4062819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.020.2649230.2205462X-RAY DIFFRACTION12.93
2.02-2.150.26061220.19582289X-RAY DIFFRACTION64.57
2.15-2.310.19041810.16053411X-RAY DIFFRACTION95.23
2.31-2.540.1841770.14833535X-RAY DIFFRACTION99.41
2.54-2.910.17511520.14643624X-RAY DIFFRACTION99.92
2.91-3.670.18441940.14633600X-RAY DIFFRACTION99.84
3.67-50.640.14721860.12023650X-RAY DIFFRACTION99.53

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