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- PDB-1qpw: CRYSTAL STRUCTURE DETERMINATION OF PORCINE HEMOGLOBIN AT 1.8A RES... -

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Basic information

Entry
Database: PDB / ID: 1qpw
TitleCRYSTAL STRUCTURE DETERMINATION OF PORCINE HEMOGLOBIN AT 1.8A RESOLUTION
Components
  • PORCINE HEMOGLOBIN (ALPHA SUBUNIT)
  • PORCINE HEMOGLOBIN (BETA SUBUNIT)
KeywordsOXYGEN TRANSPORT / X-RAY STUDY / PORCINE HEMOGLOBIN / ARTIFICIAL HUMAN BLOOD
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / hydrogen peroxide catabolic process / 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 / OXYGEN MOLECULE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLu, T.-H. / Panneerselvam, K. / Liaw, Y.-C. / Kan, P. / Lee, C.-J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure determination of porcine haemoglobin.
Authors: Lu, T.H. / Panneerselvam, K. / Liaw, Y.C. / Kan, P. / Lee, C.J.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Structure Determination of Aquomet Porcine Hemoglobin at 2.8A Resolution
Authors: Katz, D.S. / White, S.P. / Huang, W. / Kumar, R. / Christianson, D.W.
History
DepositionMay 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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_ref_seq_dif / 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_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.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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: PORCINE HEMOGLOBIN (ALPHA SUBUNIT)
B: PORCINE HEMOGLOBIN (BETA SUBUNIT)
C: PORCINE HEMOGLOBIN (ALPHA SUBUNIT)
D: PORCINE HEMOGLOBIN (BETA SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,77710
Polymers62,2474
Non-polymers2,5306
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-104 kcal/mol
Surface area23130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.10, 72.27, 114.85
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PORCINE HEMOGLOBIN (ALPHA SUBUNIT)


Mass: 15064.144 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TAIWANESE PIG FROM SLAUGHTERHOUSE / Source: (natural) Sus scrofa (pig) / References: UniProt: P01965
#2: Protein PORCINE HEMOGLOBIN (BETA SUBUNIT)


Mass: 16059.345 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: TAIWANESE PIG FROM SLAUGHTERHOUSE / Source: (natural) Sus scrofa (pig) / References: UniProt: P02067
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2.8M OF PHOSPHATE SOLUTION, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 mg/mlprotein1drop
22.8 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 10, 1991
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→8 Å / Num. all: 37481 / Num. obs: 36820 / % possible obs: 78 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 1
Reflection shellResolution: 1.8→8 Å / Rmerge(I) obs: 0.058 / % possible all: 78
Reflection
*PLUS
Num. obs: 37481
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 2 / σ(I): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3682 -RANDOM SELECTION OF 10% OF THE OBSERVED REFLECTIONS
Rwork0.207 ---
obs0.211 36820 98.2 %-
all-37481 --
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 176 574 5148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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