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- PDB-5hbi: SCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, CO-LIGANDED FORM -

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Basic information

Entry
Database: PDB / ID: 5hbi
TitleSCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, CO-LIGANDED FORM
ComponentsHEMOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRoyer Junior, W.E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity.
Authors: Pardanani, A. / Gambacurta, A. / Ascoli, F. / Royer Jr., W.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Ordered Water Molecules as Key Allosteric Mediators in a Cooperative Dimeric Hemoglobin
Authors: Royer Junior, W.E. / Pardanani, A. / Gibson, Q.H. / Peterson, E.S. / Friedman, J.M.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: A Single Mutation (Thr72-->Ile) at the Subunit Interface is Crucial for the Functional Properties of the Homodimeric Co-Operative Haemoglobin from Scapharca Inaequivalvis
Authors: Gambacurta, A. / Piro, M.C. / Coletta, M. / Clementi, M.E. / Polizio, F. / Desideri, A. / Santucci, R. / Ascoli, F.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: High-Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin
Authors: Royer Junior, W.E.
History
DepositionJun 24, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)33,2486
Polymers31,9592
Non-polymers1,2894
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-56 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.270, 43.750, 83.350
Angle α, β, γ (deg.)90.00, 121.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.425781, -0.295485, -0.855219), (-0.154335, -0.907607, 0.390423), (-0.891567, 0.298225, 0.340838)
Vector: 63.10124, -2.55875, 40.27819)

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Components

#1: Protein HEMOGLOBIN /


Mass: 15979.356 Da / Num. of mol.: 2 / Mutation: T72I
Source method: isolated from a genetically manipulated source
Details: SCAPHARCA DIMERIC HEMOGLOBIN, HEME GROUP, PROTOPORPHYRIN IX IRON
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: PGAP1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P02213
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


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


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2.3M NA/K PHOSPHATE AT PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method / Details: Royer Junior, W.E., (1994) J.Mol.Biol., 235, 657.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140-50 mg/mlhemoglobin11
22.1-2.3 Mphosphate11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 33035 / % possible obs: 87.9 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Num. measured all: 85575 / Rmerge(I) obs: 0.0617

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SDH

3sdh


Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3318 10 %RANDOM
Rwork0.194 ---
obs0.194 29717 87 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 90 193 2517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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