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- PDB-2r4y: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -

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Basic information

Entry
Database: PDB / ID: 2r4y
TitleLigand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: H69V/I114M unliganded
ComponentsGlobin-1
KeywordsOXYGEN BINDING / ALLOSTERY / OXYGEN AFFINITY / COOPERATIVE HEMOGLOBIN / OXYGEN STORAGE/TRANSPORT / Cytoplasm / Heme / Iron / Metal-binding / Oxygen transport
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / 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
PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKnapp, J.E. / Royer Jr., W.E. / Nienhaus, K. / Palladino, P. / Nienhaus, G.U.
CitationJournal: Biochemistry / Year: 2007
Title: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis
Authors: Nienhaus, K. / Knapp, J.E. / Palladino, P. / Royer Jr., W.E. / Nienhaus, G.U.
History
DepositionSep 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,1264
Polymers31,8932
Non-polymers1,2332
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.070, 44.290, 143.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 15946.325 Da / Num. of mol.: 2 / Mutation: H69V/I114M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HbI / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.19 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 8.5
Details: 1.5-2.5M PHOSPHATE, pH 8.50, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2005 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18914 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.273 / % possible all: 93.7

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4SDH

4sdh


Resolution: 2→39.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2227970.64 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 918 4.9 %RANDOM
Rwork0.176 ---
obs0.176 18914 93.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.309 Å2 / ksol: 0.339907 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å20 Å20 Å2
2---5.79 Å20 Å2
3---9.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 86 136 2448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 106 5.7 %
Rwork0.234 1754 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3param19x.hemetoph19x.heme

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