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- PDB-2grf: Crystal structure of Scapharca inaequivalvis HBI, M37V mutant in ... -

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Basic information

Entry
Database: PDB / ID: 2grf
TitleCrystal structure of Scapharca inaequivalvis HBI, M37V mutant in the absence of ligand
ComponentsGlobin-1
KeywordsOXYGEN STORAGE/TRANSPORT / INVERTEBRATE / HEMOGLOBIN / ALLOSTERY / COOPERATIVITY / OXYGEN-BINDING / OXYGEN-TRANSPORT / HEME PROTEIN / 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: 2.1 Å
AuthorsKnapp, J.E. / Pahl, R. / Srajer, V. / Royer Jr., W.E.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin.
Authors: Knapp, J.E. / Pahl, R. / Srajer, V. / Royer Jr., W.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: High Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin.
Authors: Royer Jr., W.E.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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 30, 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)33,1034
Polymers31,8702
Non-polymers1,2332
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-44 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.740, 44.510, 144.050
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: 15935.239 Da / Num. of mol.: 2 / Mutation: M37V
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): 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.: 113 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 8.5
Details: PHOSPHATE BUFFER, pH 8.50, SMALL TUBES, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 18, 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: 2.1→40 Å / Num. all: 17677 / Num. obs: 16213 / % possible obs: 90.9 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 0.089 / Net I/σ(I): 9.3
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.311 / Num. unique all: 1503 / % possible all: 86.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4SDH (DEOXY WILD TYPE HBI)

4sdh


Resolution: 2.1→30.75 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2314156.86 / 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
Rfree0.229 782 4.9 %RANDOM
Rwork0.184 ---
all0.204 17677 --
obs0.184 16104 91.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.475 Å2 / ksol: 0.32658 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2---3.75 Å20 Å2
3---5.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 86 113 2429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.891.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it5.052
X-RAY DIFFRACTIONc_scangle_it6.392.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.257 69 4.6 %
Rwork0.236 1422 -
obs--86.9 %
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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