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- PDB-1spg: CARBONMONOXY HEMOGLOBIN FROM THE TELEOST FISH LEIOSTOMUS XANTHURUS -

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Basic information

Entry
Database: PDB / ID: 1spg
TitleCARBONMONOXY HEMOGLOBIN FROM THE TELEOST FISH LEIOSTOMUS XANTHURUS
Components(HEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / CARBON MONOXIDE / R-STATE / LEIOSTOMUS XANTHURUS / TELEOST FISH / ROOT EFFECT / GLOBIN
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily ...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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesLeiostomus xanthurus (spot croaker)
MethodX-RAY DIFFRACTION / INITIAL PHASES FROM THE ISOMORPHOUS PHOSPHATE BOUND SPOT R-STATE HEMOGLOBIN (S. MYLVAGANAM, E. GETZOFF, UNPUBLISHED) / Resolution: 1.95 Å
AuthorsMylvaganam, S.E. / Getzoff, E.D.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Structural basis for the root effect in haemoglobin.
Authors: Mylvaganam, S.E. / Bonaventura, C. / Bonaventura, J. / Getzoff, E.D.
#1: Journal: J.Biol.Chem. / Year: 1976
Title: Spot Hemoglobin. Studies on the Root Effect Hemoglobin of a Marine Teleost
Authors: Bonaventura, C. / Sullivan, B. / Bonaventura, J.
History
DepositionFeb 5, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2906
Polymers32,0012
Non-polymers1,2894
Water3,153175
1
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules

A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,58012
Polymers64,0024
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13510 Å2
ΔGint-125 kcal/mol
Surface area22370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.600, 75.600, 69.700
Angle α, β, γ (deg.)90.00, 141.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHERE IS AN ALPHA-BETA DIMER IN THE ASYMMETRIC UNIT. THE ALPHA-BETA DIMERS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD THAT IS COINCIDENT WITH THE MOLECULAR TWO-FOLD OF THE ALPHA2BETA2 TETRAMER.

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Components

#1: Protein HEMOGLOBIN / SPOT HEMOGLOBIN / SPOTHBCO


Mass: 15684.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: R-STATE, CARBONMONOXY BOUND ROOT EFFECT HEMOGLOBIN / Source: (natural) Leiostomus xanthurus (spot croaker) / Tissue: BLOOD / References: UniProt: P56250
#2: Protein HEMOGLOBIN / SPOT HEMOGLOBIN / SPOTHBCO


Mass: 16316.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: R-STATE, CARBONMONOXY BOUND ROOT EFFECT HEMOGLOBIN / Source: (natural) Leiostomus xanthurus (spot croaker) / Tissue: BLOOD / References: UniProt: P56251
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.01 MTris-HCl11
30.01 Mcalcium acetate11
2PEG600011

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Data collection

DiffractionMean temperature: 293.15 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1993
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.95 Å / Num. obs: 16125 / % possible obs: 76 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6
Reflection shellResolution: 1.95→2.07 Å / % possible all: 38
Reflection
*PLUS
Num. measured all: 27397
Reflection shell
*PLUS
% possible obs: 38 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: INITIAL PHASES FROM THE ISOMORPHOUS PHOSPHATE BOUND SPOT R-STATE HEMOGLOBIN (S. MYLVAGANAM, E. GETZOFF, UNPUBLISHED)
Resolution: 1.95→10 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.245 -2 %
Rwork0.191 --
obs0.191 13623 65.4 %
Displacement parametersBiso mean: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 90 175 2518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.687
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
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 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76

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