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- PDB-6hal: Human carbonmonoxy hemoglobin SFX dataset -

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Basic information

Entry
Database: PDB / ID: 6hal
TitleHuman carbonmonoxy hemoglobin SFX dataset
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / human carbonmonoxy Hemoglobin / R-state / SFX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsDoak, B. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Gruenbein, M.L. / Hilpert, M. / Kloos, M. / Nass Kovacs, G. / Roome, C.M. / Shoeman, R.L. ...Doak, B. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Gruenbein, M.L. / Hilpert, M. / Kloos, M. / Nass Kovacs, G. / Roome, C.M. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. / Sherrell, D.A. / Owen, R.L. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Crystallography on a chip - without the chip: sheet-on-sheet sandwich.
Authors: Doak, R.B. / Nass Kovacs, G. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Grunbein, M.L. / Hilpert, M. / Kloos, M. / Roome, C.M. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. ...Authors: Doak, R.B. / Nass Kovacs, G. / Gorel, A. / Foucar, L. / Barends, T.R.M. / Grunbein, M.L. / Hilpert, M. / Kloos, M. / Roome, C.M. / Shoeman, R.L. / Stricker, M. / Tono, K. / You, D. / Ueda, K. / Sherrell, D.A. / Owen, R.L. / Schlichting, I.
History
DepositionAug 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94812
Polymers61,3704
Non-polymers2,5788
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-121 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 157.400, 64.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14894.027 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: erythrocyte / Organ: blood / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15791.067 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7
Details: batch crystallization, using 1.6 M Na/K phosphate, neutal pH as precipitant

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.7 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 9, 2017 / Details: KB mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.2→39.35 Å / Num. obs: 29516 / % possible obs: 99.9 % / Redundancy: 1 % / Biso Wilson estimate: 42.37 Å2 / CC1/2: 0.98 / R split: 0.115 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2R splitDiffraction-ID% possible all
2.2-2.26121580.6540.4661100
2.26-2.32121061100
2.32-2.39120291100
2.39-2.46119811100
2.46-2.54119171100
2.54-2.63118591100
2.63-2.73117821100
2.73-2.84117491100
2.84-2.97116671100
2.97-3.11115931100
3.11-3.28115431100
3.28-3.48114321100
3.48-3.72113621100
3.72-4.02112821100
4.02-4.4111711100
4.4-4.92110731100
4.92-5.6819661100
5.68-6.9618221100
6.96-9.841642198.9
9.84-39.351382196.7

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.24data extraction
CrystFEL0.6.3data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180126data scaling
Coot0.8.9.1model building
REFMAC5.8.0189phasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2DN2

2dn2


Resolution: 2.2→39.35 Å / Cor.coef. Fo:Fc: 0.9427 / Cor.coef. Fo:Fc free: 0.9276 / SU R Cruickshank DPI: 0.253 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.245 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.182
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 1542 5.22 %RANDOM
Rwork0.1825 ---
obs0.184 29515 99.96 %-
Displacement parametersBiso mean: 43.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.637 Å20 Å20 Å2
2---0.6404 Å20 Å2
3----2.9966 Å2
Refine analyzeLuzzati coordinate error obs: 0.279 Å
Refinement stepCycle: 1 / Resolution: 2.2→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 180 20 4532
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014652HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.986378HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes720HARMONIC5
X-RAY DIFFRACTIONt_it4652HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.18
X-RAY DIFFRACTIONt_other_torsion19.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion560SEMIHARMONIC5
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_contact4718SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2451 157 5.52 %
Rwork0.2278 2687 -
all0.2287 2844 -
obs--100 %
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)
12.267-0.04480.24221.6054-0.44951.9797-0.0015-0.03670.0023-0.08070.06360.03770.1387-0.2269-0.0621-0.1886-0.02920.0004-0.16130.0609-0.1687-9.4723-30.933624.813
22.24750.6703-0.37961.8668-0.43191.3880.0453-0.1260.27530.0917-0.01140.0305-0.12780.0909-0.0339-0.1719-0.0158-0.0192-0.1832-0.0153-0.15837.8979-14.170229.3724
31.7695-0.73410.79921.5925-0.20371.55110.02270.2226-0.1246-0.0218-0.03710.05710.16410.27250.0144-0.17420.02140.0324-0.124-0.0346-0.191510.3541-27.45020.01
42.77480.128-0.40181.3195-0.39841.485-0.05860.06890.17260.00120.05760.1069-0.2208-0.12620.0011-0.16210.0176-0.0252-0.19840.0313-0.1551-6.4276-9.46231.0745
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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