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- PDB-1gcw: CO form hemoglobin from mustelus griseus -

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Basic information

Entry
Database: PDB / ID: 1gcw
TitleCO form hemoglobin from mustelus griseus
Components(PROTEIN (HEMOGLOBIN)) x 2
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / CARBON MONOXIDE BOUND FORM / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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 beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesMustelus griseus (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNaoi, Y. / Chong, K.T. / Yoshimatsu, K. / Miyazaki, G. / Tame, J.R.H. / Park, S.Y. / Adachi, S.I. / Morimoto, H.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The functional similarity and structural diversity of human and cartilaginous fish hemoglobins.
Authors: Naoi, Y. / Chong, K.T. / Yoshimatsu, K. / Miyazaki, G. / Tame, J.R. / Park, S.Y. / Adachi, S. / Morimoto, H.
History
DepositionAug 8, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (HEMOGLOBIN)
B: PROTEIN (HEMOGLOBIN)
C: PROTEIN (HEMOGLOBIN)
D: PROTEIN (HEMOGLOBIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,87912
Polymers62,3014
Non-polymers2,5788
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.700, 80.450, 114.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (HEMOGLOBIN)


Mass: 15319.614 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Mustelus griseus (fish) / Cell: RED BLOOD CELL / Tissue: BLOOD / References: UniProt: Q9YGW2
#2: Protein PROTEIN (HEMOGLOBIN)


Mass: 15831.082 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Mustelus griseus (fish) / Cell: RED BLOOD CELL / Tissue: BLOOD / References: UniProt: Q9YGW1
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 7
Details: PEG2000, sodium phosphate, hydro sulfide, pH 7.00, SMALL TUBES, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %(w/v)PEG200011
250 mMsodium phosphate11
32 %protein11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 255405 / % possible obs: 91.5 % / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.265 / % possible all: 66.4
Reflection
*PLUS
Num. obs: 39951 / Num. measured all: 260718
Reflection shell
*PLUS
% possible obs: 66.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.255 1963 RANDOM
Rwork0.199 --
obs0.199 37342 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 172 63 4503
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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