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- PDB-3uma: Crystal structure of a hypothetical peroxiredoxin protein frm Sin... -

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Basic information

Entry
Database: PDB / ID: 3uma
TitleCrystal structure of a hypothetical peroxiredoxin protein frm Sinorhizobium meliloti
ComponentsHypothetical peroxiredoxin protein
KeywordsOXIDOREDUCTASE / NYSGRC / PSI Biology / Structural Genomics / New York Structural Genomics Research Consortium
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
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione-dependent peroxiredoxin
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical peroxiredoxin protein from Sinorhizobium meliloti
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionNov 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical peroxiredoxin protein
B: Hypothetical peroxiredoxin protein
C: Hypothetical peroxiredoxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3384
Polymers60,2423
Non-polymers961
Water1,33374
1
A: Hypothetical peroxiredoxin protein


Theoretical massNumber of molelcules
Total (without water)20,0811
Polymers20,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical peroxiredoxin protein


Theoretical massNumber of molelcules
Total (without water)20,0811
Polymers20,0811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical peroxiredoxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1772
Polymers20,0811
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Hypothetical peroxiredoxin protein

A: Hypothetical peroxiredoxin protein


Theoretical massNumber of molelcules
Total (without water)40,1612
Polymers40,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area14570 Å2
MethodPISA
5
B: Hypothetical peroxiredoxin protein
C: Hypothetical peroxiredoxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2573
Polymers40,1612
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-21 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.063, 113.063, 98.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-184-

HOH

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Components

#1: Protein Hypothetical peroxiredoxin protein


Mass: 20080.689 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: R00915, SMc00072 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92RF9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M Ammonium Sulfate, 0.1M HEPES, PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 37257 / Num. obs: 37257 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.388 / Num. unique all: 3689 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WFC

2wfc


Resolution: 2.2→48.96 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.733 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.206 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1847 5 %RANDOM
Rwork0.21293 ---
obs0.21428 35280 99.53 %-
all-35280 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.888 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 5 74 3754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223746
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9655079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60824.412136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56815622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2381515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212751
X-RAY DIFFRACTIONr_mcbond_it0.6891.52442
X-RAY DIFFRACTIONr_mcangle_it1.31523894
X-RAY DIFFRACTIONr_scbond_it2.37731304
X-RAY DIFFRACTIONr_scangle_it3.6594.51185
LS refinement shellResolution: 2.203→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 126 -
Rwork0.235 2504 -
obs-1847 97.66 %

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