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- PDB-1nm3: Crystal structure of Heamophilus influenza hybrid-Prx5 -

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Basic information

Entry
Database: PDB / ID: 1nm3
TitleCrystal structure of Heamophilus influenza hybrid-Prx5
ComponentsProtein HI0572
KeywordsELECTRON TRANSPORT / hybrid / peroxiredoxin / glutaredoxin
Function / homology
Function and homology information


glutathione-dependent peroxiredoxin / thioredoxin peroxidase activity / cell redox homeostasis / hydrogen peroxide catabolic process / cellular response to oxidative stress / cytoplasm
Similarity search - Function
Glutaredoxin domain / Peroxiredoxin-5-like / Glutaredoxin subgroup / Redoxin / Redoxin / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. ...Glutaredoxin domain / Peroxiredoxin-5-like / Glutaredoxin subgroup / Redoxin / Redoxin / Glutaredoxin active site / Glutaredoxin active site. / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hybrid peroxiredoxin hyPrx5
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsKim, S.J. / Woo, J.R. / Hwang, Y.S. / Jeong, D.G. / Shin, D.H. / Kim, K.H. / Ryu, S.E.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The Tetrameric Structure of Haemophilus influenza Hybrid Prx5 Reveals Interactions between Electron Donor and Acceptor Proteins.
Authors: Kim, S.J. / Woo, J.R. / Hwang, Y.S. / Jeong, D.G. / Shin, D.H. / Kim, K. / Ryu, S.E.
History
DepositionJan 8, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein HI0572
B: Protein HI0572
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6846
Polymers54,2992
Non-polymers3844
Water00
1
A: Protein HI0572
B: Protein HI0572
hetero molecules

A: Protein HI0572
B: Protein HI0572
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,36712
Polymers108,5994
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9930 Å2
ΔGint-130 kcal/mol
Surface area41790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.854, 72.854, 229.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein HI0572 / hybrid peroxiredoxin


Mass: 27149.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: P44758
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate, sodium acetate, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.6 Mammonium sulfate1reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoirpH8.0
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 6059 / Num. obs: 15821 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→99 Å / % possible all: 98.5
Reflection
*PLUS
Num. obs: 15906 / Num. measured all: 407938 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 100 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→99 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.283 770 random
Rwork0.239 --
obs0.239 15821 -
all-16059 -
Refinement stepCycle: LAST / Resolution: 2.8→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 20 0 3736
Refinement
*PLUS
Lowest resolution: 99 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83

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