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- PDB-4yox: Crystal structure of a trimeric exonuclease PhoExo I from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 4yox
TitleCrystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 in complex with poly-dT
Components
  • 3-5 exonuclease PhoExo I
  • 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
KeywordsHYDROLASE/DNA / exonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


exonuclease activity / metal ion binding
Similarity search - Function
Protein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / 3-5 exonuclease PhoExo I
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsMiyazono, K. / Ito, T. / Tanokura, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science, and Technology Japan
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for substrate recognition and processive cleavage mechanisms of the trimeric exonuclease PhoExo I
Authors: Miyazono, K. / Ishino, S. / Tsutsumi, K. / Ito, T. / Ishino, Y. / Tanokura, M.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-5 exonuclease PhoExo I
B: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
C: 3-5 exonuclease PhoExo I
D: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'
E: 3-5 exonuclease PhoExo I
F: 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)84,9116
Polymers84,9116
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-49 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.737, 94.755, 105.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-5 exonuclease PhoExo I


Mass: 26219.281 Da / Num. of mol.: 3 / Mutation: D80N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: A0A060P168
#2: DNA chain 5'-D(*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2084.392 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: MES, PEG6000, LiCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→70.392 Å / Num. all: 60017 / Num. obs: 60017 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 35.55 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Rsym value: 0.078 / Net I/av σ(I): 8.504 / Net I/σ(I): 16.2 / Num. measured all: 435374
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.167.40.8670.96436186770.3420.8672.5100
2.16-2.297.40.6071.36071881680.2390.6073.5100
2.29-2.457.40.4281.85744077350.1690.4284.9100
2.45-2.657.40.2892.75354372100.1140.2897100
2.65-2.97.40.1744.54945166690.0680.17410.7100
2.9-3.247.40.098.64440660300.0360.0918.6100
3.24-3.747.20.05114.23853853670.020.05131100
3.74-4.586.80.036183106845690.0150.03644.3100
4.58-6.486.50.03119.82328435860.0130.03147.3100
6.48-19.7616.30.02524.61256520060.010.02554.796.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 2.05→19.761 Å / FOM work R set: 0.7993 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 25.39 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2075 5801 5.06 %
Rwork0.1788 108759 -
obs0.1803 59922 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.68 Å2 / Biso mean: 65.52 Å2 / Biso min: 26.38 Å2
Refinement stepCycle: final / Resolution: 2.05→19.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5328 240 0 151 5719
Biso mean---50.58 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085685
X-RAY DIFFRACTIONf_angle_d1.1677727
X-RAY DIFFRACTIONf_chiral_restr0.048886
X-RAY DIFFRACTIONf_plane_restr0.006937
X-RAY DIFFRACTIONf_dihedral_angle_d11.9612174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.07330.35072040.347136163820
2.0733-2.09770.36781780.332936533831
2.0977-2.12320.31361990.312435893788
2.1232-2.150.30671950.302537003895
2.15-2.17830.36532120.29735653777
2.1783-2.20810.32022000.272736573857
2.2081-2.23960.28371730.2635883761
2.2396-2.2730.27852060.24736303836
2.273-2.30850.25851800.249436373817
2.3085-2.34620.29941520.235336353787
2.3462-2.38660.27121960.229636593855
2.3866-2.430.26052330.224535843817
2.43-2.47660.22931980.216235793777
2.4766-2.52710.23912180.201836063824
2.5271-2.58190.21141870.191936343821
2.5819-2.64180.21711970.197736353832
2.6418-2.70770.23061850.192936483833
2.7077-2.78070.24461910.195136073798
2.7807-2.86230.22911860.185136193805
2.8623-2.95440.19832020.181936383840
2.9544-3.05970.22121910.173236163807
3.0597-3.18170.19081720.177236253797
3.1817-3.32580.1931720.172936643836
3.3258-3.50030.22021990.17636223821
3.5003-3.71820.2032290.161236233852
3.7182-4.00310.17891950.149735743769
4.0031-4.40190.17041900.137136453835
4.4019-5.02970.16222000.130236363836
5.0297-6.30260.19251540.151536483802
6.3026-19.7620.14342070.139236273834
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.45290.59061.47772.9448-0.13012.3342-0.19150.20130.4246-0.1575-0.06310.0223-0.2643-0.14610.15120.25020.0261-0.03440.36960.0470.482719.762430.25976.1668
24.32090.81291.33034.4478-0.7492.8232-0.17370.35460.3592-0.0850.1020.2493-0.2907-0.34130.15970.2660.0682-0.02680.50120.01350.474916.413628.78282.468
36.64161.65342.64996.36121.70315.3888-0.32760.62971.0546-0.9276-0.1811-0.0183-1.0635-0.39330.13270.35020.0467-0.06330.60270.10010.68526.710330.30941.2907
44.0166-0.6210.85332.796-0.59552.4529-0.2962-0.47630.78780.30990.12740.4464-0.4795-0.62680.12640.36710.0897-0.02140.6454-0.07780.75691.493729.801613.5883
53.64610.14840.24882.1264-0.27651.83770.04080.6089-0.1368-0.1512-0.0346-0.1064-0.02910.0410.03890.24250.0003-0.03570.3958-0.02470.395325.514723.42263.1604
63.7577-0.58920.27622.39170.44743.13560.0030.90030.4245-0.2716-0.0805-0.1871-0.34990.11010.11360.2344-0.0355-0.01420.41820.06670.46735.375729.5963.9954
77.56310.7413-0.63772.8534-1.11591.9559-0.1852-0.85631.28460.5706-0.17410.5439-0.1927-0.6449-0.00520.44970.069-0.01680.5629-0.12270.879917.686332.950716.1034
82.9170.02520.96032.8488-1.08533.1415-0.0396-0.4106-0.07290.7355-0.0193-0.3502-0.1870.08290.05470.4547-0.0075-0.13070.2723-0.0160.492943.153923.97132.689
92.84740.05980.95773.29620.3622.5787-0.0361-0.54220.42750.8007-0.03180.2415-0.2064-0.22250.26520.5525-0.0069-0.06740.3689-0.06670.739237.149139.840633.575
102.3772-0.72750.14412.5106-0.4351.794-0.0304-0.2998-0.4440.39320.0663-0.26930.1640.174-0.10920.344-0.0164-0.1150.25010.04740.549843.520513.175528.4857
113.362-0.20511.50866.068-0.94413.7790.1376-1.20630.59531.5014-0.22540.7294-0.5231-0.37630.03890.9062-0.0354-0.03970.5334-0.03510.88731.621324.773236.75
121.6336-0.0439-0.28592.2607-0.08081.22570.201-0.4442-1.29480.29220.21880.64480.2725-0.6301-0.21440.477-0.1993-0.00820.64410.32581.079612.76082.137626.7444
133.19481.70890.18281.78720.36930.51110.1508-0.9196-1.15610.4350.21620.56270.8559-0.5176-0.11320.7133-0.2086-0.07990.48250.32621.20524.0231-4.661931.244
143.59090.30221.31881.1954-1.45772.54790.3645-1.2584-0.43120.46410.22710.83140.1925-1.002-0.05180.5977-0.23920.12381.29320.34871.5291.06912.564628.1221
152.8714-0.31591.0842.0332-0.54471.84620.1903-0.9553-0.26591.1022-0.10231.00340.211-1.024-0.25320.92-0.1370.23081.1490.31311.051415.06395.711743.1047
162.29920.11440.55961.7864-0.56792.11660.1181-1.175-0.44060.7081-0.06050.90870.1832-1.0619-0.18520.6818-0.17010.15581.0080.27361.100613.84133.642437.8567
170.86820.9940.52021.75740.1681.75730.38110.0858-0.95670.2202-0.08120.24510.9072-0.2844-0.26650.5268-0.1291-0.15130.40280.00540.993319.96071.035517.692
181.36161.22191.32723.77861.28731.52110.36360.3363-1.5279-0.59330.1109-0.03870.9654-0.0164-0.37130.8569-0.1753-0.29240.41470.0331.361920.5428-8.342517.8102
193.13880.3630.17382.9447-0.0013.08050.3362-0.1688-1.137-0.24650.07060.39060.6337-0.557-0.24680.4168-0.0943-0.10880.43960.01710.913813.04975.255611.7858
202.76730.08211.07870.85630.12951.44980.095-0.9541-0.20770.67710.57431.0099-0.6069-1.7553-0.02580.730.00290.19390.85120.25780.975810.156811.908929.2662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 55 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 72 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 138 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 200 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 229 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 4 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 55 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 56 through 138 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 139 through 229 )C0
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 4 )D0
12X-RAY DIFFRACTION12chain 'E' and (resid 1 through 30 )E0
13X-RAY DIFFRACTION13chain 'E' and (resid 31 through 44 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 45 through 55 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 56 through 102 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 103 through 159 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 160 through 192 )E0
18X-RAY DIFFRACTION18chain 'E' and (resid 193 through 207 )E0
19X-RAY DIFFRACTION19chain 'E' and (resid 208 through 227 )E0
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 4 )F0

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