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- PDB-3u5r: Crystal structure of a hypothetical protein SMc02350 from Sinorhi... -

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Basic information

Entry
Database: PDB / ID: 3u5r
TitleCrystal structure of a hypothetical protein SMc02350 from Sinorhizobium meliloti 1021
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / hypothetical protein / SMc02350
Function / homology
Function and homology information


antioxidant activity / oxidoreductase activity
Similarity search - Function
: / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin domain-containing protein
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAgarwal, R. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein SMc02350 from Sinorhizobium meliloti 1021
Authors: Agarwal, R. / Almo, S.C. / Swaminathan, S.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: uncharacterized protein
F: uncharacterized protein
G: uncharacterized protein
H: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)94,0614
Polymers94,0614
Non-polymers00
Water7,116395
1
E: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
F: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
G: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
H: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.657, 58.567, 85.476
Angle α, β, γ (deg.)82.65, 83.58, 66.29
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
uncharacterized protein


Mass: 23515.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02577, SMc02350 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q92MN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M tri sodium citrate pH 5.6, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2011 / Details: mirrors
RadiationMonochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 59768 / Num. obs: 59768 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5 / Num. unique all: 5911 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
ARP/wARPmodel building
Cootmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2YWI

2ywi


Resolution: 2.05→34.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.724 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2321 3026 5.1 %RANDOM
Rwork0.18192 ---
obs0.18445 56737 97.79 %-
all-59768 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å20.01 Å2
2---0.02 Å20.02 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5586 0 0 395 5981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0225704
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9547750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5924.109258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98715844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4441535
X-RAY DIFFRACTIONr_chiral_restr0.1550.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214455
X-RAY DIFFRACTIONr_mcbond_it1.2421.53681
X-RAY DIFFRACTIONr_mcangle_it2.22625840
X-RAY DIFFRACTIONr_scbond_it3.72532023
X-RAY DIFFRACTIONr_scangle_it5.864.51910
LS refinement shellResolution: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 219 -
Rwork0.234 4091 -
obs--95.19 %

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