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- PDB-2aup: Residue F4 plays a key role in modulating oxygen affinity and coo... -

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Basic information

Entry
Database: PDB / ID: 2aup
TitleResidue F4 plays a key role in modulating oxygen affinity and cooperativity in Scapharca dimeric hemoglobin
ComponentsGlobin I
KeywordsOXYGEN STORAGE/TRANSPORT / allostery / oxygen binding / oxygen affinity / cooperative 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: 1.8 Å
AuthorsKnapp, J.E. / Bonham, M.A. / Gibson, Q.H. / Nichols, J.C. / Royer Jr., W.E.
CitationJournal: 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.
History
DepositionAug 28, 2005Deposition site: RCSB / Processing site: RCSB
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 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 1.4Aug 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)33,2004
Polymers31,9672
Non-polymers1,2332
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-47 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.130, 44.330, 143.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsdimer formed by the A and B chains within the asymmetric unit

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Components

#1: Protein Globin I / Dimeric hemoglobin / HBI


Mass: 15983.304 Da / Num. of mol.: 2 / Mutation: F97Y
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.: 188 / 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: 2.08 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 8.5 / Details: Phosphate, 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 31, 2000 / Details: Yale Mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→26.7 Å / Num. all: 27782 / Num. obs: 24393 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.321 / % possible all: 78.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4SDH

4sdh


Resolution: 1.8→26.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1807500.16 / 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
Rfree0.205 4566 18.7 %RANDOM
Rwork0.18 ---
all0.191 27782 --
obs0.18 24393 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.8966 Å2 / ksol: 0.353101 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 86 188 2517
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.712.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.29 399 18.8 %
Rwork0.289 1729 -
obs-2128 78.2 %
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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