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- PDB-4hrr: Scapharca tetrameric hemoglobin, CO-state -

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Basic information

Entry
Database: PDB / ID: 4hrr
TitleScapharca tetrameric hemoglobin, CO-state
Components
  • Globin-2 A chain
  • Hemoglobin B chain
KeywordsOXYGEN TRANSPORT / hemoglobin / Globin fold / Oxygen
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
: / Myoglobin-like, M family globin domain / 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 B chain / Globin-2 A chain / Globin-2 B chain
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsRoyer, W.E.
Citation
Journal: Biochemistry / Year: 2013
Title: Tertiary and Quaternary Allostery in Tetrameric Hemoglobin from Scapharca inaequivalvis.
Authors: Ronda, L. / Bettati, S. / Henry, E.R. / Kashav, T. / Sanders, J.M. / Royer, W.E. / Mozzarelli, A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The 2.0 A crystal structure of Scapharca tetrameric hemoglobin: cooperative dimers within an allosteric tetramer.
Authors: Royer, W.E. / Heard, K.S. / Harrington, D.J. / Chiancone, E.
History
DepositionOct 28, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 13, 2013ID: 1SCT
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 8, 2014Group: Database references
Revision 1.3Sep 20, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Globin-2 A chain
B: Hemoglobin B chain
C: Globin-2 A chain
D: Hemoglobin B chain
E: Globin-2 A chain
F: Hemoglobin B chain
G: Globin-2 A chain
H: Hemoglobin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,67824
Polymers130,5228
Non-polymers5,15616
Water35,7421984
1
A: Globin-2 A chain
B: Hemoglobin B chain
C: Globin-2 A chain
D: Hemoglobin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83912
Polymers65,2614
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-127 kcal/mol
Surface area22570 Å2
MethodPISA
2
E: Globin-2 A chain
F: Hemoglobin B chain
G: Globin-2 A chain
H: Hemoglobin B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,83912
Polymers65,2614
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-125 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.537, 99.884, 125.242
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
Globin-2 A chain / Globin II A chain / HBII-A


Mass: 16153.610 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Blood Clam / Source: (natural) Scapharca inaequivalvis (ark clam) / Strain: Scapharca inaequivalvis / References: UniProt: P14821
#2: Protein
Hemoglobin B chain


Mass: 16476.887 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: blood clam / Source: (natural) Scapharca inaequivalvis (ark clam) / Strain: Scapharca inaequivalvis / References: UniProt: O02480, UniProt: P14822*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1984 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE AUTHORS DECLARE THAT THE CRYSTALLIZED SEQUENCE IS PERHAPS AN ISOFORM OF THE REGISTERED SEQUENCE ...THE AUTHORS DECLARE THAT THE CRYSTALLIZED SEQUENCE IS PERHAPS AN ISOFORM OF THE REGISTERED SEQUENCE IN THE DATA BASE REFERENCE.

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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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 5.8
Details: 1.9-2.2M Na/K Phosphate, pH 5.8, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. all: 321447 / Num. obs: 321447 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 29.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SCT

1sct
PDB Unreleased entry


Resolution: 1.25→11.79 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.822 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17421 14225 5 %RANDOM
Rwork0.13738 ---
obs0.13921 271903 89.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.25→11.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 360 1984 11482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210012
X-RAY DIFFRACTIONr_angle_refined_deg1.416213916
X-RAY DIFFRACTIONr_angle_other_deg0.805322982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37851354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16224.376425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.017151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2481568
X-RAY DIFFRACTIONr_chiral_restr0.0730.21559
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211945
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022403
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr2.893320262
X-RAY DIFFRACTIONr_sphericity_free37.145268
X-RAY DIFFRACTIONr_sphericity_bonded11.493521714
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 908 -
Rwork0.206 17697 -
obs--80.56 %

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