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- PDB-1fsx: THE X-RAY STRUCTURE DETERMINATION OF BOVINE CARBONMONOXY HB AT 2.... -

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Basic information

Entry
Database: PDB / ID: 1fsx
TitleTHE X-RAY STRUCTURE DETERMINATION OF BOVINE CARBONMONOXY HB AT 2.1 A RESOLUTION AND ITS RELATIONSHIP TO THE QUATERNARY STRUCTURE OF OTHER HB CRYSTAL FORMS
Components
  • HEMOGLOBIN ALPHA CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / Hemoglobin Tetramer / R-State / Quaternary Structure / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / organic acid binding / 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 domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSafo, M.K. / Abraham, D.J.
CitationJournal: Protein Sci. / Year: 2001
Title: The X-ray structure determination of bovine carbonmonoxy hemoglobin at 2.1 A resoultion and its relationship to the quaternary structures of other hemoglobin crystal froms.
Authors: Safo, M.K. / Abraham, D.J.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: 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 7, 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_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_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_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_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 ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
C: HEMOGLOBIN ALPHA CHAIN
D: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,68712
Polymers62,1094
Non-polymers2,5788
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-113 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.41, 110.63, 65.40
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a tetramer in the asymmetric unit.

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Components

#1: Protein HEMOGLOBIN ALPHA CHAIN


Mass: 15077.171 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: BLOOD / References: UniProt: P01966
#2: Protein HEMOGLOBIN BETA CHAIN


Mass: 15977.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: BLOOD / References: UniProt: P02070
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 46.8 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.3
Details: Potassium phosphate, sodium phosphate, pyridine, benzene, pH 7.3, LIQUID DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: batch method / PH range low: 7.4 / PH range high: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 %protein11
23.6 Mphosphate11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 20, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→64.5 Å / Num. all: 122102 / Num. obs: 32949 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Num. unique all: 2301 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 122102
Reflection shell
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.42

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.1→64.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: 1. Anomalous data used for refinement. 2. Bulk Solvent Correction during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1647 -random
Rwork0.205 ---
all0.208 32949 --
obs0.208 32949 100 %-
Refinement stepCycle: LAST / Resolution: 2.1→64.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 180 136 4702
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d1.73
X-RAY DIFFRACTIONx_dihedral19.49
X-RAY DIFFRACTIONx_improper1.38
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 64.5 Å / σ(F): 0 / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

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