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- PDB-2av3: F97L- no ligand -

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Basic information

Entry
Database: PDB / ID: 2av3
TitleF97L- no ligand
ComponentsGlobin I
KeywordsOXYGEN STORAGE/TRANSPORT / Allosteric / oxygen binding / oxygen transport / hemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
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: 1.7 Å
AuthorsKnapp, J.E. / Bonham, M.A. / Gibson, Q.H. / Nichols, J.C. / Royer Jr., W.E.
Citation
Journal: Biochemistry / Year: 2005
Title: Residue F4 plays a key role in modulating oxygen affinity and cooperativity in Scapharca dimeric hemoglobin
Authors: Knapp, J.E. / Bonham, M.A. / Gibson, Q.H. / Nichols, J.C. / Royer Jr., W.E.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Mutation of residue PHE97 to Leu disrupts the central allosteric pathway in Scapharca dimeric hemoglobin.
Authors: Pardanani, A. / Gibson, Q.H. / Colotti, G. / Royer Jr., W.E.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2006ID: 2HBI
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 20, 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 1.6Aug 23, 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 I
B: Globin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1004
Polymers31,8672
Non-polymers1,2332
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-45 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.990, 44.270, 143.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe A and B chains form a dimeric assembly that is the functional biological unit.

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Components

#1: Protein Globin I / Dimeric hemoglobin / HBI


Mass: 15933.286 Da / Num. of mol.: 2 / Mutation: F97L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: pcs-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110lacIq L8 / 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.: 174 / 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: 2.1 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 8.5
Details: Phosphate buffer, pH 8.5, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 14, 1995 / Details: Collimator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→10 Å / Num. all: 32599 / Num. obs: 27416 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073
Reflection shellResolution: 1.7→1.76 Å / % possible all: 69.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4SDH

4sdh


Resolution: 1.7→9.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1385052.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1338 4.9 %RANDOM
Rwork0.184 ---
all0.191 32599 --
obs0.184 27416 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.4121 Å2 / ksol: 0.345133 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.32 Å20 Å20 Å2
2---2.5 Å20 Å2
3----2.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→9.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 86 174 2486
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it0.711.5
X-RAY DIFFRACTIONc_mcangle_it1.072
X-RAY DIFFRACTIONc_scbond_it1.422
X-RAY DIFFRACTIONc_scangle_it2.132.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.291 126 5.6 %
Rwork0.293 2120 -
obs-2241 69.7 %
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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