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- PDB-5sw7: Structure of the Human Hemoglobin Mutant Hb Providence (A-Gly-C:V... -

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Basic information

Entry
Database: PDB / ID: 5sw7
TitleStructure of the Human Hemoglobin Mutant Hb Providence (A-Gly-C:V1M; B,D:V1M,K82D; Ferrous, carbonmonoxy bound)
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Heme / distal histidine / oxidative stability
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 / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.851 Å
AuthorsSoman, J. / Olson, J.S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01-HL110900 United States
Robert A. Welch FoundationC0612 United States
National Institute of Food and Agriculture (NIFA, United States) United States
CitationJournal: To Be Published
Title: Structure of the Human Hemoglobin Mutant Hb Providence (A-Gly-C:V1M; B,D:V1M,K82D; Ferrous, carbonmonoxy bound)
Authors: Soman, J. / Olson, J.S.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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 1.4Oct 4, 2023Group: 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)32,5327
Polymers31,1482
Non-polymers1,3845
Water2,954164
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)65,06314
Polymers62,2954
Non-polymers2,76810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13080 Å2
ΔGint-133 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.381, 53.381, 192.743
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-388-

HOH

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Components

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Hemoglobin subunit ... , 2 types, 2 molecules AB

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


Mass: 15239.470 Da / Num. of mol.: 1 / Mutation: V1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Beta-globin / Hemoglobin beta chain


Mass: 15908.171 Da / Num. of mol.: 1 / Mutation: V1M,K82D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871

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Non-polymers , 4 types, 169 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGly142 was engineered into the sequence of the alpha chain to form a linker between the two alpha ...Gly142 was engineered into the sequence of the alpha chain to form a linker between the two alpha chains A and C.

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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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 296 K / Method: batch mode / pH: 6.7 / Details: 2.5M sodium/potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→29.72 Å / Num. obs: 24374 / % possible obs: 98.4 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.022 / Net I/σ(I): 26
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.2 / CC1/2: 0.89 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2DN3.pdb

2dn3


Resolution: 1.851→29.715 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1993 8.18 %
Rwork0.1857 --
obs0.1887 24374 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.851→29.715 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2195 0 95 164 2454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072440
X-RAY DIFFRACTIONf_angle_d0.8223348
X-RAY DIFFRACTIONf_dihedral_angle_d13.4041391
X-RAY DIFFRACTIONf_chiral_restr0.053357
X-RAY DIFFRACTIONf_plane_restr0.006424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8513-1.89750.39951390.341557X-RAY DIFFRACTION98
1.8975-1.94880.33271370.27891546X-RAY DIFFRACTION100
1.9488-2.00620.31811430.26241603X-RAY DIFFRACTION100
2.0062-2.07090.27691420.2331580X-RAY DIFFRACTION100
2.0709-2.14490.24411410.2021587X-RAY DIFFRACTION100
2.1449-2.23080.27161430.19591600X-RAY DIFFRACTION99
2.2308-2.33220.24321390.19571579X-RAY DIFFRACTION99
2.3322-2.45520.23771410.18251595X-RAY DIFFRACTION99
2.4552-2.60890.2241440.18971607X-RAY DIFFRACTION100
2.6089-2.81020.22911430.18891623X-RAY DIFFRACTION99
2.8102-3.09270.22791460.19821618X-RAY DIFFRACTION100
3.0927-3.53960.24011430.18261607X-RAY DIFFRACTION97
3.5396-4.45710.20231370.14811538X-RAY DIFFRACTION91
4.4571-29.71840.18081550.18111741X-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)
12.8765-0.0561-0.14682.938-0.22731.6087-0.1044-0.03660.01590.11740.1281-0.1610.01530.1031-0.01530.3199-0.00510.01250.2543-0.02080.229835.028134.440515.3159
22.5401-0.3749-0.50081.6707-0.27394.0988-0.01750.2655-0.12820.0401-0.05120.30290.0417-0.50860.04680.2115-0.0010.05470.3202-0.02370.301412.483132.86467.0819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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