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- PDB-5ker: Deer mouse recombinant hemoglobin from high altitude species -

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Basic information

Entry
Database: PDB / ID: 5ker
TitleDeer mouse recombinant hemoglobin from high altitude species
Components
  • Alpha-globin
  • Beta globin
KeywordsTRANSPORT PROTEIN / oxygen-transport
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / organic acid binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Alpha-globin / Beta-globin
Similarity search - Component
Biological speciesPeromyscus maniculatus (North American deer mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsInoguchi, N. / Natarajan, C. / Storz, J.F. / Moriyama, H.
CitationJournal: PLoS ONE / Year: 2017
Title: Alteration of the alpha 1 beta 2/ alpha 2 beta 1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice.
Authors: Inoguchi, N. / Mizuno, N. / Baba, S. / Kumasaka, T. / Natarajan, C. / Storz, J.F. / Moriyama, H.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Derived calculations
Revision 1.3Sep 27, 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
C: Alpha-globin
D: Beta globin
E: Alpha-globin
F: Beta globin
G: Alpha-globin
H: Beta globin
A: Alpha-globin
B: Beta globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,65316
Polymers122,7218
Non-polymers4,9328
Water12,448691
1
C: Alpha-globin
D: Beta globin
A: Alpha-globin
B: Beta globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8268
Polymers61,3604
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10710 Å2
ΔGint-109 kcal/mol
Surface area22930 Å2
MethodPISA
2
E: Alpha-globin
F: Beta globin
G: Alpha-globin
H: Beta globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8268
Polymers61,3604
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-109 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.182, 229.618, 53.277
Angle α, β, γ (deg.)90.00, 119.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-globin / Alpha-globin subunit / Hemoglobin alpha chain / Hemoglobin alpha subunit 2 / Hemoglobin alpha-subunit


Mass: 14893.987 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse)
Gene: HBA, Hba, HBAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZQ87
#2: Protein
Beta globin / Beta-globin / Beta-globin subunit / HBB-T1 / HBB-T2


Mass: 15786.198 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse)
Gene: HBB, HBB-T1, HBB-T2 / Production host: Escherichia coli (E. coli) / References: UniProt: B7SBL4
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop
Details: 26% (w/v) PEG 3350 in 50 mM sodium/potassium phosphate, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→29.56 Å / Num. obs: 65478 / % possible obs: 71 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.10.1_2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H2L

4h2l


Resolution: 2.202→29.56 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 21.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2017 2004 5.03 %
Rwork0.193 --
obs0.1935 39853 71.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.202→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8604 0 344 691 9639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069220
X-RAY DIFFRACTIONf_angle_d0.85212608
X-RAY DIFFRACTIONf_dihedral_angle_d18.7573120
X-RAY DIFFRACTIONf_chiral_restr0.0551356
X-RAY DIFFRACTIONf_plane_restr0.0051560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2021-2.25710.35691190.33622180X-RAY DIFFRACTION58
2.2571-2.31810.28321100.2992344X-RAY DIFFRACTION61
2.3181-2.38630.31031310.28772359X-RAY DIFFRACTION63
2.3863-2.46330.3061240.28342387X-RAY DIFFRACTION63
2.4633-2.55130.25751420.24212468X-RAY DIFFRACTION65
2.5513-2.65340.20291340.19792466X-RAY DIFFRACTION65
2.6534-2.77410.17971250.19542529X-RAY DIFFRACTION67
2.7741-2.92020.19291460.20572547X-RAY DIFFRACTION68
2.9202-3.1030.19981510.20752669X-RAY DIFFRACTION70
3.103-3.34230.21111490.19362847X-RAY DIFFRACTION74
3.3423-3.6780.19471710.16973065X-RAY DIFFRACTION82
3.678-4.2090.17621600.15273219X-RAY DIFFRACTION84
4.209-5.29790.14691780.14653336X-RAY DIFFRACTION87
5.2979-29.56240.16921640.16733433X-RAY DIFFRACTION89

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