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- PDB-3qob: Mechanical Coupling Controls Cooperative Ligand Binding in a Homo... -

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Basic information

Entry
Database: PDB / ID: 3qob
TitleMechanical Coupling Controls Cooperative Ligand Binding in a Homodimeric Hemoglobin
ComponentsGlobin-1
KeywordsOXYGEN TRANSPORT / time-resolved / Laue diffraction / dynamic crystallography / heterogeneous structure
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 domain 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 speciesAnadara inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsRen, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures.
Authors: Ren, Z. / Srajer, V. / Knapp, J.E. / Royer Jr., W.E.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Globin-1
B: Globin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2226
Polymers31,9332
Non-polymers1,2894
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-52 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.250, 43.980, 83.500
Angle α, β, γ (deg.)90.000, 122.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Globin-1 / Dimeric hemoglobin / Globin I / HbI


Mass: 15966.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Anadara inaequivalvis (ark clam) / References: UniProt: P02213
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO

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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: 2.27 Å3/Da / Density % sol: 45.88 %

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.017 - 1.2
DetectorType: MAR CCD 165 mm / Detector: AREA DETECTOR / Date: Nov 6, 2008
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0171
21.21
ReflectionResolution: 1.6→38.2 Å / Num. all: 27862 / Num. obs: 27844 / % possible obs: 74.5 % / Observed criterion σ(F): 6 / Redundancy: 3.27 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.0597 / Net I/σ(I): 24.7

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Processing

Software
NameClassification
LaueCollectdata collection
dynamiXmodel building
dynamiXrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3SDH

3sdh


Resolution: 1.6→38.2 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 6 / Stereochemistry target values: Engh & Huber /
Num. reflection% reflection
all27862 -
obs27844 74.5 %
Displacement parametersBiso max: 20 Å2 / Biso mean: 20 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 90 0 2322

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