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- PDB-2o6k: Crystal structure of UPF0346 from Staphylococcus aureus. Northeas... -

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Basic information

Entry
Database: PDB / ID: 2o6k
TitleCrystal structure of UPF0346 from Staphylococcus aureus. Northeast Structural Genomics target ZR218.
ComponentsUPF0346 protein MW1311
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ZR218 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Protein of unknown function UPF0346 / YozE SAM-like / YozE SAM-like domain / YozE SAM-like superfamily / YozE SAM-like fold / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UPF0346 protein MW1311 / UPF0346 protein in crr 3'region
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBenach, J. / Abashidze, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Baran, M.C. / Acton, T.B. ...Benach, J. / Abashidze, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of UPF0346 from Staphylococcus aureus. Northeast Structural Genomics target ZR218.
Authors: Benach, J. / Abashidze, M. / Seetharaman, J. / Wang, D. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0346 protein MW1311
B: UPF0346 protein MW1311


Theoretical massNumber of molelcules
Total (without water)20,1832
Polymers20,1832
Non-polymers00
Water1,47782
1
A: UPF0346 protein MW1311


Theoretical massNumber of molelcules
Total (without water)10,0921
Polymers10,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0346 protein MW1311


Theoretical massNumber of molelcules
Total (without water)10,0921
Polymers10,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.223, 52.157, 115.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe AU contains the biological unit consisting of subunits A & B.

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Components

#1: Protein UPF0346 protein MW1311


Mass: 10091.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: MW1311 / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7BEF3, UniProt: Q7A0W3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 300mM NH4F, 50mM MES pH 6.5, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97916, 0.97949, 0.96863
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979161
20.979491
30.968631
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
6117.41192480.1041.792.11991299.6
5.9213.81180860.1072.012.12012799.6
5.8312.1883310.1292.472.31529199.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.525099.410.0591.0496.2
3.594.5299.810.0631.1166.4
3.143.5910010.0741.0716.4
2.853.1499.910.0991.1736.3
2.652.8599.610.1251.1626.3
2.492.6510010.1671.1046
2.372.4999.410.2141.2135.9
2.262.3799.510.3967.2645
2.182.269910.3081.7685.7
2.12.1899.910.4151.9875.7
4.525099.520.061.136.3
3.594.5299.920.0641.0376.4
3.143.5910020.0791.1916.4
2.853.1499.920.111.2896.2
2.652.8599.720.1481.2576.1
2.492.6510020.1961.4885.8
2.372.4999.420.2662.1565.7
2.262.3799.420.4978.0414.9
2.182.2698.820.4172.5025.5
2.12.1899.820.5933.1275.5
4.955099.430.071.2456.3
3.934.9599.930.0821.5826.4
3.443.9399.930.0981.5176.4
3.123.4499.930.1191.4996.1
2.93.1299.830.171.7275.9
2.732.910030.2141.7885.8
2.592.7399.530.2922.0475.5
2.482.5999.930.3822.5935.4
2.382.4899.130.5022.8215.3
2.32.3899.330.66310.0274.7
ReflectionResolution: 2.1→50 Å / Num. obs: 19912 / % possible obs: 99.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.104 / Χ2: 1.786 / Net I/σ(I): 17.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.185.70.41519561.987199.9
2.18-2.265.70.30819981.768199
2.26-2.3750.39619827.264199.5
2.37-2.495.90.21419961.213199.4
2.49-2.6560.16720031.1041100
2.65-2.856.30.12519661.162199.6
2.85-3.146.30.09920061.173199.9
3.14-3.596.40.07420001.0711100
3.59-4.526.40.06319951.116199.8
4.52-506.20.05920101.049199.4

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Phasing

Phasing dmFOM : 0.67 / FOM acentric: 0.69 / FOM centric: 0.58 / Reflection: 10146 / Reflection acentric: 8399 / Reflection centric: 1747
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.4910.850.90.77508312196
3.7-60.870.90.7614771131346
3-3.70.820.850.6918351502333
2.6-30.690.710.5717751501274
2.2-2.60.580.60.4128202442378
2.1-2.20.430.460.2217311511220

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
RESOLVE2.08phasing
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / FOM work R set: 0.878 / σ(F): 295 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.217 1771 8.9 %
Rwork0.208 --
obs-18638 93.9 %
Solvent computationBsol: 41.674 Å2
Displacement parametersBiso mean: 23.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.108 Å20 Å20 Å2
2---1.887 Å20 Å2
3---1.778 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 82 1340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4951.5
X-RAY DIFFRACTIONc_scbond_it2.3172
X-RAY DIFFRACTIONc_mcangle_it2.3782
X-RAY DIFFRACTIONc_scangle_it3.6432.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 35

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.120.313540.24426480
2.12-2.140.285570.219433490
2.14-2.160.26480.217460508
2.16-2.190.27410.226466507
2.19-2.210.253540.196497551
2.21-2.240.284650.211452517
2.24-2.260.252570.202432489
2.26-2.290.211350.198350385
2.29-2.320.288480.317477525
2.32-2.350.328270.209373400
2.35-2.380.307500.228489539
2.38-2.410.234520.214493545
2.41-2.450.323470.243473520
2.45-2.490.219630.229473536
2.49-2.530.178440.214481525
2.53-2.570.316460.229495541
2.57-2.620.232580.222493551
2.62-2.670.172500.193498548
2.67-2.720.222400.216498538
2.72-2.780.256430.241505548
2.78-2.850.194630.222490553
2.85-2.920.227580.213523581
2.92-30.116350.211506541
3-3.090.231450.226504549
3.09-3.190.246490.211516565
3.19-3.30.278480.234514562
3.3-3.430.194410.198510551
3.43-3.590.159610.185515576
3.59-3.770.16660.181500566
3.77-4.010.187590.181490549
4.01-4.310.201590.172496555
4.31-4.740.171590.174506565
4.74-5.420.2490.186512561
5.42-6.780.211460.231512558
6.78-200.197540.189509563
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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