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- PDB-3dex: Crystal structure of SAV_2001 protein from Streptomyces avermitil... -

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Basic information

Entry
Database: PDB / ID: 3dex
TitleCrystal structure of SAV_2001 protein from Streptomyces avermitilis, Northeast Structural Genomics Consortium Target SvR107.
ComponentsSAV_2001
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologySelenoprotein, Rdx-type / Rdx family / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Selenoprotein W-related protein
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Chen, C.X. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Chen, C.X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of SAV_2001 protein from Streptomyces avermitilis, Northeast Structural Genomics Consortium Target SvR107.
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owen, L.A. / Chen, C.X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAV_2001
B: SAV_2001
C: SAV_2001
D: SAV_2001
E: SAV_2001
F: SAV_2001
G: SAV_2001
H: SAV_2001


Theoretical massNumber of molelcules
Total (without water)99,5458
Polymers99,5458
Non-polymers00
Water00
1
A: SAV_2001
B: SAV_2001


Theoretical massNumber of molelcules
Total (without water)24,8862
Polymers24,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-5 kcal/mol
Surface area8030 Å2
MethodPISA
2
C: SAV_2001
D: SAV_2001


Theoretical massNumber of molelcules
Total (without water)24,8862
Polymers24,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-3 kcal/mol
Surface area7860 Å2
MethodPISA
3
E: SAV_2001
F: SAV_2001


Theoretical massNumber of molelcules
Total (without water)24,8862
Polymers24,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-5 kcal/mol
Surface area7830 Å2
MethodPISA
4
G: SAV_2001
H: SAV_2001


Theoretical massNumber of molelcules
Total (without water)24,8862
Polymers24,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.126, 158.318, 48.088
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological assembly is possibly dimer.

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Components

#1: Protein
SAV_2001


Mass: 12443.153 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: SAV2001, SAV_2001 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q82LK9
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: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 14% PEG 3350, 0.15 M K/Na-tartrate, and 10% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Details: mirrors.
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 41024 / Num. obs: 39958 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.101 / Net I/σ(I): 12.42
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.58 / Rsym value: 0.524 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OKA

2oka


Resolution: 2.7→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 567738.9 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3213 9.7 %RANDOM
Rwork0.23 ---
obs0.23 33121 85.2 %-
all-38874 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9882 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.59 Å20 Å23.53 Å2
2---13.4 Å20 Å2
3---6.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5209 0 0 0 5209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.344 227 9.6 %
Rwork0.296 2136 -
obs--61.1 %

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