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- PDB-3nl7: Human Hemoglobin A mutant beta H63W carbonmonoxy-form -

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Basic information

Entry
Database: PDB / ID: 3nl7
TitleHuman Hemoglobin A mutant beta H63W carbonmonoxy-form
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Hemoglobin / ligand migration pathways
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / 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 / blood microparticle / ficolin-1-rich granule lumen / 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 family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family 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 / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Blocking the gate to ligand entry in human hemoglobin.
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3786
Polymers31,0892
Non-polymers1,2894
Water5,314295
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)64,75512
Polymers62,1774
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11850 Å2
ΔGint-113 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.210, 53.210, 191.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21A-222-

HOH

31A-225-

HOH

41B-260-

HOH

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Components

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


Mass: 15150.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Hemoglobin beta chain / Beta-globin / LVV-hemorphin-7


Mass: 15938.263 Da / Num. of mol.: 1 / Mutation: H63W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P68871
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 6.7
Details: Protein Solution (20mg/ml protein in 0.01 M phosphate pH 7.0) mixed with mother liquor (3.4 M Na/K phosphate, pH6.7) for final concentrations of 2.3 M Na/K phosphate, SMALL TUBES, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 17, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→51.27 Å / Num. all: 26616 / Num. obs: 25409 / % possible obs: 95.5 % / Observed criterion σ(I): 3 / Redundancy: 3.74 % / Rmerge(I) obs: 0.074 / Χ2: 0.99 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 98.8 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.26 / Χ2: 0.99

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.1_357)refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DN3

2dn3


Resolution: 1.8→31.115 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1973 7.88 %RANDOM
Rwork0.186 ---
obs0.1897 25026 94.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.933 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0751 Å2-0 Å20 Å2
2---2.0751 Å2-0 Å2
3---4.1502 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 90 295 2581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0282400
X-RAY DIFFRACTIONf_angle_d1.2813301
X-RAY DIFFRACTIONf_dihedral_angle_d13.119818
X-RAY DIFFRACTIONf_chiral_restr0.066354
X-RAY DIFFRACTIONf_plane_restr0.007412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.27971410.18911670X-RAY DIFFRACTION97
1.845-1.89490.2591430.1821682X-RAY DIFFRACTION98
1.8949-1.95060.24251450.18151684X-RAY DIFFRACTION99
1.9506-2.01360.26391420.18281675X-RAY DIFFRACTION99
2.0136-2.08550.25281450.18581680X-RAY DIFFRACTION98
2.0855-2.1690.23041410.18171660X-RAY DIFFRACTION96
2.169-2.26770.22821390.16941605X-RAY DIFFRACTION94
2.2677-2.38720.22621390.16761628X-RAY DIFFRACTION93
2.3872-2.53670.24351380.17531621X-RAY DIFFRACTION92
2.5367-2.73250.25771370.17551603X-RAY DIFFRACTION93
2.7325-3.00730.25471390.18831602X-RAY DIFFRACTION90
3.0073-3.44190.24951300.18271516X-RAY DIFFRACTION86
3.4419-4.33460.18221330.15961536X-RAY DIFFRACTION85
4.3346-31.11940.2051610.18591891X-RAY DIFFRACTION97
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)
10.65450.2416-0.04740.20430.07340.2815-0.09940.0339-0.0005-0.01460.1025-0.04430.01650.01940.00610.1875-0.0040.02860.1371-0.00710.135235.344934.715815.3157
20.9389-0.1359-0.04960.18060.01370.5698-0.04070.0886-0.03610.0151-0.05560.11260.0185-0.16180.07940.1316-0.01350.03320.1551-0.02550.150212.525333.00137.0793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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