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- PDB-1it3: Hagfish CO ligand hemoglobin -

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Basic information

Entry
Database: PDB / ID: 1it3
TitleHagfish CO ligand hemoglobin
Componentshemoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / hagfish / Eptatretus burgeri / CO form / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding
Similarity search - Function
Globin, lamprey/hagfish type / Myoglobin-like, M family globin domain / 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 / Globin-F1
Similarity search - Component
Biological speciesEptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMito, M. / Chong, K.T. / Park, S.-Y. / Tame, J.R.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of deoxy- and carbonmonoxyhemoglobin F1 from the hagfish Eptatretus burgeri
Authors: Mito, M. / Chong, K.T. / Miyazaki, G. / Adachi, S. / Park, S.-Y. / Tame, J.R. / Morimoto, H.
History
DepositionJan 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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_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 1.4Nov 20, 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
C: hemoglobin
D: hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,03612
Polymers67,4584
Non-polymers2,5788
Water4,864270
1
A: hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5093
Polymers16,8651
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5093
Polymers16,8651
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5093
Polymers16,8651
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5093
Polymers16,8651
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.973, 150.636, 51.943
Angle α, β, γ (deg.)90.00, 106.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hemoglobin


Mass: 16864.525 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Eptatretus burgeri (inshore hagfish) / References: UniProt: Q7SID0
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 6.5
Details: PEG 4000, Tris-Buffer, pH 6.5, SMALL TUBES, temperature 298K
Crystal grow
*PLUS
Temperature: 27 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
121 %PEG400011
210 %glycerol11
350 mMBis-Tris-HCl11pH6.5
40.020 mM2-mercaptoethanol11
5100 mM11NaCl
61.5 %protein11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2000 / Details: mirrors
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 73549 / Num. obs: 32410 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.181 / % possible all: 63.9
Reflection
*PLUS
% possible obs: 83.2 % / Num. measured all: 73549 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F5O

1f5o


Resolution: 2.1→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1641 5.06 %RANDOM
Rwork0.196 ---
obs-32399 84.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 180 270 5210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_improper_angle_d1.04
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.303 199 -
Rwork0.272 --
obs-4271 66.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.06 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.04
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.272

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