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- PDB-5woh: Human Hemoglobin Immersed in Liquid Oxygen for 20 seconds -

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Basic information

Entry
Database: PDB / ID: 5woh
TitleHuman Hemoglobin Immersed in Liquid Oxygen for 20 seconds
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN BINDING / Oxygen / Hemoglobin
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / regulation of blood pressure / oxygen binding / 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4508
Polymers60,9844
Non-polymers2,4664
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-103 kcal/mol
Surface area23950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.430, 83.120, 83.680
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
21chain C
12(chain B and (resid 1 through 25 or resid 27 through 146))
22(chain D and (resid 1 through 25 or resid 27 through 146))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA2 - 142
211chain CC2 - 142
112(chain B and (resid 1 through 25 or resid 27 through 146))B1 - 25
122(chain B and (resid 1 through 25 or resid 27 through 146))B27 - 146
212(chain D and (resid 1 through 25 or resid 27 through 146))D1 - 25
222(chain D and (resid 1 through 25 or resid 27 through 146))D27 - 146

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


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


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
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: 1.32→37.715 Å / Num. obs: 72681 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.151 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.108 / Χ2: 1.025 / Net I/σ(I): 14.17 / Num. measured all: 1747662 / Scaling rejects: 1270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.32-1.3513.3452.071.4290020.5432.1599.4
1.35-1.3914.0811.6461.9287590.6831.70799.1
1.39-1.4314.141.442.3385400.7581.49399.3
1.43-1.4814.1991.1063.2483200.8611.14799.6
1.48-1.5214.2560.8734.3180540.9130.90599.5
1.52-1.5814.3390.7085.5278370.9490.73499.6
1.58-1.6414.4050.5696.8575840.9670.5999.7
1.64-1.714.4490.4548.3672820.9770.47199.8
1.7-1.7814.4840.34710.4969910.9850.3699.8
1.78-1.8714.5110.25713.1266960.9910.26699.8
1.87-1.9714.4630.18217.0563990.9940.18999.9
1.97-2.0914.3780.13121.8760600.9960.136100
2.09-2.2314.2170.10326.0356860.9970.10799.9
2.23-2.4114.1720.08729.1253250.9970.09100
2.41-2.6414.1840.07631.6649260.9980.079100
2.64-2.9514.0820.06835.0444750.9980.07100
2.95-3.4113.7540.0638.2739720.9980.062100
3.41-4.1713.6530.05241.1333880.9990.054100
4.17-5.913.5950.0541.9126630.9990.052100
5.9-37.71512.460.06439.9915460.9980.06799.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
XSCALEdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DN1

2dn1


Resolution: 1.58→37.715 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 19.64
RfactorNum. reflection% reflection
Rfree0.2071 1997 2.89 %
Rwork0.1824 --
obs0.1831 69026 94.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.5 Å2 / Biso mean: 21.8582 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.58→37.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 172 702 5178
Biso mean--17.76 29.62 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074625
X-RAY DIFFRACTIONf_angle_d0.8996351
X-RAY DIFFRACTIONf_chiral_restr0.051691
X-RAY DIFFRACTIONf_plane_restr0.007794
X-RAY DIFFRACTIONf_dihedral_angle_d13.4842623
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1228X-RAY DIFFRACTION6.397TORSIONAL
12C1228X-RAY DIFFRACTION6.397TORSIONAL
21B1327X-RAY DIFFRACTION6.397TORSIONAL
22D1327X-RAY DIFFRACTION6.397TORSIONAL
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 (%)
1.58-1.60.23621300.20034262439285
1.6-1.6210.21781190.19914203432285
1.621-1.64320.22581360.19774356449286
1.6432-1.66670.23371310.20114452458388
1.6667-1.69160.27511240.20734432455689
1.6916-1.7180.22731430.2064453459689
1.718-1.74620.21441340.20464544467891
1.7462-1.77630.25181280.20344599472791
1.7763-1.80860.23891450.19964632477792
1.8086-1.84340.21281320.20064640477293
1.8434-1.8810.18671440.20114634477894
1.881-1.92190.24471370.19984779491695
1.9219-1.96660.20831440.19624853499796
1.9666-2.01580.2311430.19864837498097
2.0158-2.07030.25841370.19464949508698
2.0703-2.13120.20641440.17984961510599
2.1312-2.20.18561490.17874967511699
2.2-2.27860.20691530.18694906505998
2.2786-2.36980.19831420.17824976511899
2.3698-2.47770.20341500.18424953510399
2.4777-2.60830.22831590.193950095168100
2.6083-2.77160.22111490.186349655114100
2.7716-2.98550.22131500.185250205170100
2.9855-3.28580.21541460.180950055151100
3.2858-3.76090.17511540.163150295183100
3.7609-4.73690.16031440.143549825126100
4.7369-37.72570.20971610.188150055166100

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