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- PDB-5wog: Human Hemoglobin immersed in Liquid Oxygen for 1 minute -

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Basic information

Entry
Database: PDB / ID: 5wog
TitleHuman Hemoglobin immersed in Liquid Oxygen for 1 minute
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN BINDING / Hemoglobin / Oxygen
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin 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 / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / 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 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGumpper, R.H. / Terrell, J.R. / Luo, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Hemoglobin crystals immersed in liquid oxygen reveal diffusion channels.
Authors: Terrell, J.R. / Gumpper, R.H. / Luo, M.
History
DepositionAug 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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 alpha
C: Hemoglobin subunit beta
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4508
Polymers60,9844
Non-polymers2,4664
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10270 Å2
ΔGint-100 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.360, 82.890, 83.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 2 through 84 or (resid 85...
12(chain C and (resid 1 through 140 or resid 142 through 146))
22(chain D and (resid 1 through 89 or (resid 90...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA2 - 142
211(chain B and (resid 2 through 84 or (resid 85...B2 - 84
221(chain B and (resid 2 through 84 or (resid 85...B85
231(chain B and (resid 2 through 84 or (resid 85...B2 - 142
241(chain B and (resid 2 through 84 or (resid 85...B2 - 142
251(chain B and (resid 2 through 84 or (resid 85...B2 - 142
261(chain B and (resid 2 through 84 or (resid 85...B2 - 142
112(chain C and (resid 1 through 140 or resid 142 through 146))C1 - 140
122(chain C and (resid 1 through 140 or resid 142 through 146))C142 - 146
212(chain D and (resid 1 through 89 or (resid 90...D1 - 89
222(chain D and (resid 1 through 89 or (resid 90...D90
232(chain D and (resid 1 through 89 or (resid 90...D1 - 147
242(chain D and (resid 1 through 89 or (resid 90...D1 - 147
252(chain D and (resid 1 through 89 or (resid 90...D1 - 147
262(chain D and (resid 1 through 89 or (resid 90...D1 - 147

NCS ensembles :
ID
1
2

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Components

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


Mass: 14601.673 Da / Num. of mol.: 2 / 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.: 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 277.15 K / Method: batch mode
Details: 1 mL of 40 mg/mL hemoglobin + 2.65 M (final concentration) phosphate buffer, topped with 100 uL toluene

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.26→41.445 Å / Num. obs: 140708 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 13.699 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.118 / Χ2: 1.013 / Net I/σ(I): 11.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.26-1.2912.784.2880.63103650.3834.46599.9
1.29-1.3312.9812.5451.12100540.4932.64999.9
1.33-1.3713.1982.4761.2598400.5762.57599.9
1.37-1.4113.3771.8281.8494920.6891.999.9
1.41-1.4513.5721.4722.5392660.8271.52999.7
1.45-1.5113.7621.0513.6389110.8981.09199.4
1.51-1.5613.8980.7585.0185830.9350.78799.3
1.56-1.6314.0940.5676.2682780.9660.58899.1
1.63-1.714.1990.4277.8879260.9770.44399.2
1.7-1.7814.2870.30810.1575860.9850.3299
1.78-1.8814.3430.22712.872080.990.23598.8
1.88-1.9914.0650.17117.1968100.9930.17798.2
1.99-2.1314.0410.12121.6864870.9960.12699.6
2.13-2.313.7160.10424.9360320.9960.10899
2.3-2.5214.0460.08328.0156000.9980.08699.8
2.52-2.8214.0280.07431.0250900.9980.077100
2.82-3.2513.8130.06634.4645330.9980.068100
3.25-3.9813.6430.05937.1538590.9980.06199.9
3.98-5.6313.7270.05438.3830290.9980.05699.9
5.63-41.44512.8230.06836.8617590.9970.07199.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DN1

2dn1


Resolution: 1.54→41.445 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 19.12
RfactorNum. reflection% reflection
Rfree0.2065 1987 2.76 %
Rwork0.184 --
obs0.1846 136945 91.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.46 Å2 / Biso mean: 21.3023 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.54→41.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 172 777 5241
Biso mean--18.18 30.38 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074611
X-RAY DIFFRACTIONf_angle_d0.8766333
X-RAY DIFFRACTIONf_chiral_restr0.051692
X-RAY DIFFRACTIONf_plane_restr0.007790
X-RAY DIFFRACTIONf_dihedral_angle_d13.0292615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1222X-RAY DIFFRACTION7.738TORSIONAL
12B1222X-RAY DIFFRACTION7.738TORSIONAL
21C1317X-RAY DIFFRACTION7.738TORSIONAL
22D1317X-RAY DIFFRACTION7.738TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5401-1.55960.25951210.22134239436079
1.5596-1.58010.23661240.20674246437079
1.5801-1.60170.24331240.21194397452181
1.6017-1.62460.21081250.20854362448781
1.6246-1.64890.24371260.20284437456383
1.6489-1.67460.23841370.2084525466283
1.6746-1.70210.25221220.19944555467785
1.7021-1.73140.23551270.20444602472985
1.7314-1.76290.25921270.21014653478087
1.7629-1.79680.27511470.20284732487988
1.7968-1.83350.2511400.20684821496189
1.8335-1.87340.23251260.20054815494189
1.8734-1.9170.20061440.20534933507792
1.917-1.96490.22151370.19974967510492
1.9649-2.0180.20391430.19195135527896
2.018-2.07740.24291430.1865239538297
2.0774-2.14450.20541520.18275224537697
2.1445-2.22110.18281450.18025146529195
2.2211-2.310.22991440.1915212535697
2.31-2.41510.21011510.17855317546899
2.4151-2.54250.23991480.18495343549199
2.5425-2.70170.21641550.19455319547499
2.7017-2.91030.19511630.183453895552100
2.9103-3.2030.19631540.179353875541100
3.203-3.66630.20871520.164853875539100
3.6663-4.61820.14291540.151853815535100
4.6182-41.460.18761500.18654015551100

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