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- PDB-3mpr: Crystal Structure of endonuclease/exonuclease/phosphatase family ... -

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Basic information

Entry
Database: PDB / ID: 3mpr
TitleCrystal Structure of endonuclease/exonuclease/phosphatase family protein from Bacteroides thetaiotaomicron, Northeast Structural Genomics Consortium Target BtR318A
ComponentsPutative endonuclease/exonuclease/phosphatase family protein
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


3'-5'-RNA exonuclease activity / endonuclease activity
Similarity search - Function
Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / BROMIDE ION / DI(HYDROXYETHYL)ETHER / Unknown ligand / Endonuclease/exonuclease/phosphatase family protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.899 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target BtR318A
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / ...Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative endonuclease/exonuclease/phosphatase family protein
B: Putative endonuclease/exonuclease/phosphatase family protein
C: Putative endonuclease/exonuclease/phosphatase family protein
D: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,08334
Polymers138,3924
Non-polymers1,69130
Water22,0141222
1
A: Putative endonuclease/exonuclease/phosphatase family protein
B: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,01521
Polymers69,1962
Non-polymers81919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Putative endonuclease/exonuclease/phosphatase family protein
D: Putative endonuclease/exonuclease/phosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,06813
Polymers69,1962
Non-polymers87211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.643, 103.143, 79.811
Angle α, β, γ (deg.)90.00, 103.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative endonuclease/exonuclease/phosphatase family protein


Mass: 34597.898 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3783 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8A183

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Non-polymers , 5 types, 1252 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 8 / Source method: obtained synthetically
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1222 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:LiBr 0.1M, NaAcetate 0.1M, PEG8000 20% v/v, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97909 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 94601 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 16.18 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.899→39.474 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 19.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 4742 5.01 %
Rwork0.156 --
obs0.1584 94569 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.29 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1738 Å20 Å2-0.3088 Å2
2--4.6256 Å20 Å2
3----1.4518 Å2
Refinement stepCycle: LAST / Resolution: 1.899→39.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9021 0 60 1222 10303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069403
X-RAY DIFFRACTIONf_angle_d1.05512708
X-RAY DIFFRACTIONf_dihedral_angle_d13.4773413
X-RAY DIFFRACTIONf_chiral_restr0.0841281
X-RAY DIFFRACTIONf_plane_restr0.0051672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8992-1.92070.27181500.23432836X-RAY DIFFRACTION95
1.9207-1.94330.24941590.20232995X-RAY DIFFRACTION99
1.9433-1.9670.24421380.17912955X-RAY DIFFRACTION99
1.967-1.99190.22091520.16792956X-RAY DIFFRACTION99
1.9919-2.01810.22961480.16363015X-RAY DIFFRACTION99
2.0181-2.04580.2371510.16522996X-RAY DIFFRACTION99
2.0458-2.0750.21981810.17472946X-RAY DIFFRACTION99
2.075-2.1060.21431590.16472978X-RAY DIFFRACTION99
2.106-2.13890.25191310.15422998X-RAY DIFFRACTION100
2.1389-2.1740.221700.15412980X-RAY DIFFRACTION100
2.174-2.21140.22511610.15113011X-RAY DIFFRACTION100
2.2114-2.25160.20891590.16972975X-RAY DIFFRACTION99
2.2516-2.29490.21981510.16762953X-RAY DIFFRACTION99
2.2949-2.34180.21211510.15142986X-RAY DIFFRACTION100
2.3418-2.39270.20891660.14563006X-RAY DIFFRACTION100
2.3927-2.44840.181520.14772988X-RAY DIFFRACTION100
2.4484-2.50960.22851560.15343009X-RAY DIFFRACTION100
2.5096-2.57740.21141420.15453026X-RAY DIFFRACTION100
2.5774-2.65320.20321630.14972988X-RAY DIFFRACTION100
2.6532-2.73890.20061730.15182993X-RAY DIFFRACTION100
2.7389-2.83670.21411570.15333027X-RAY DIFFRACTION100
2.8367-2.95030.20661480.15063029X-RAY DIFFRACTION100
2.9503-3.08450.19561570.14922996X-RAY DIFFRACTION100
3.0845-3.2470.17991790.14212974X-RAY DIFFRACTION100
3.247-3.45040.17871570.14773040X-RAY DIFFRACTION100
3.4504-3.71660.17541520.13763025X-RAY DIFFRACTION100
3.7166-4.09020.16691560.13283018X-RAY DIFFRACTION100
4.0902-4.68130.1731790.12373029X-RAY DIFFRACTION100
4.6813-5.89480.16881720.1393026X-RAY DIFFRACTION100
5.8948-39.48260.21631720.19153073X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 48.0088 Å / Origin y: 43.2709 Å / Origin z: 24.1992 Å
111213212223313233
T0.001 Å2-0.0051 Å20.0031 Å2-0.007 Å20.0022 Å2--0.0049 Å2
L0.0645 °20.0261 °20.0261 °2-0.0828 °2-0.0275 °2--0.0919 °2
S0.001 Å °-0.0205 Å °0.0006 Å °0 Å °0.0053 Å °0.0055 Å °0.0176 Å °-0.0252 Å °-0.0065 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 1311
2X-RAY DIFFRACTION1allB2 - 1232
3X-RAY DIFFRACTION1allC1 - 1310
4X-RAY DIFFRACTION1allD3 - 1311
5X-RAY DIFFRACTION1all1 - 33
6X-RAY DIFFRACTION1allU1 - 8
7X-RAY DIFFRACTION1allF1 - 15

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