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- PDB-4h2l: Deer mouse hemoglobin in hydrated format -

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Basic information

Entry
Database: PDB / ID: 4h2l
TitleDeer mouse hemoglobin in hydrated format
Components
  • Alpha-globinHemoglobin subunit alpha
  • Beta globin
KeywordsOXYGEN TRANSPORT / Hemoglobin
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
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
PROTOPORPHYRIN IX CONTAINING FE / Alpha-globin / Beta-globin
Similarity search - Component
Biological speciesPeromyscus maniculatus (North American deer mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.779 Å
AuthorsInoguchi, N. / Oshlo, J.R. / Natarajan, C. / Weber, R.E. / Fago, A. / Storz, J.F. / Moriyama, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix.
Authors: Inoguchi, N. / Oshlo, J.R. / Natarajan, C. / Weber, R.E. / Fago, A. / Storz, J.F. / Moriyama, H.
History
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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: Alpha-globin
B: Beta globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0354
Polymers30,8022
Non-polymers1,2332
Water7,837435
1
A: Alpha-globin
B: Beta globin
hetero molecules

A: Alpha-globin
B: Beta globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0708
Polymers61,6054
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area11030 Å2
ΔGint-93 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.675, 80.061, 86.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-513-

HOH

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Components

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


Mass: 14940.015 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse)
Gene: HBA / Production host: Escherichia coli (E. coli) / References: UniProt: A4ZQ95
#2: Protein Beta globin / Beta-globin subunit


Mass: 15862.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peromyscus maniculatus (North American deer mouse)
Gene: HBB-T1, HBB-T2 / Production host: Escherichia coli (E. coli) / References: UniProt: C5MQT7
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 42.66 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% (w/v) PEG 3350 in 50 mM sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2012
RadiationMonochromator: blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.779→29.433 Å / % possible obs: 98.53 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.7→1.9 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.779→29.433 Å / SU ML: 0.17 / σ(F): 0.16 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 1981 7.85 %
Rwork0.1619 --
obs0.165 25236 97.01 %
all-25631 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.779→29.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 86 435 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072324
X-RAY DIFFRACTIONf_angle_d1.0643177
X-RAY DIFFRACTIONf_dihedral_angle_d13.022790
X-RAY DIFFRACTIONf_chiral_restr0.069343
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7787-1.82310.2651340.20051573X-RAY DIFFRACTION94
1.8231-1.87240.23391400.16421601X-RAY DIFFRACTION95
1.8724-1.92750.20171360.15621614X-RAY DIFFRACTION96
1.9275-1.98970.20741440.16651625X-RAY DIFFRACTION96
1.9897-2.06080.1921410.14991657X-RAY DIFFRACTION97
2.0608-2.14330.19581380.15251651X-RAY DIFFRACTION97
2.1433-2.24080.19751370.14811650X-RAY DIFFRACTION98
2.2408-2.35890.22771490.1571651X-RAY DIFFRACTION98
2.3589-2.50660.20751380.15791677X-RAY DIFFRACTION98
2.5066-2.70.21141460.16511689X-RAY DIFFRACTION99
2.7-2.97150.20941430.16641710X-RAY DIFFRACTION99
2.9715-3.40090.2111440.16381699X-RAY DIFFRACTION99
3.4009-4.28270.14831440.14711716X-RAY DIFFRACTION98
4.2827-29.43650.21191470.1811742X-RAY DIFFRACTION96

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