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

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Basic information

Entry
Database: PDB / ID: 4yor
TitleCrystal structure of a trimeric exonuclease PhoExo I from Pyrococcus horikoshii OT3 at 1.52A resolution.
Components3-5 exonuclease PhoExo I
KeywordsHYDROLASE / exonuclease
Function / homologyProtein of unknown function DUF4152 / Protein of unknown function DUF4152 / Protein of unknown function (DUF4152) / exonuclease activity / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / metal ion binding / Alpha Beta / 3-5 exonuclease PhoExo I
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.52 Å
AuthorsMiyazono, K. / Tsutsumi, K. / 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 / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: 3-5 exonuclease PhoExo I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3844
Polymers51,3352
Non-polymers492
Water6,954386
1
A: 3-5 exonuclease PhoExo I
hetero molecules

A: 3-5 exonuclease PhoExo I
hetero molecules

A: 3-5 exonuclease PhoExo I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0766
Polymers77,0033
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5420 Å2
ΔGint-46 kcal/mol
Surface area28390 Å2
MethodPISA
2
B: 3-5 exonuclease PhoExo I
hetero molecules

B: 3-5 exonuclease PhoExo I
hetero molecules

B: 3-5 exonuclease PhoExo I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0766
Polymers77,0033
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5300 Å2
ΔGint-42 kcal/mol
Surface area28270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.065, 112.065, 202.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21B-448-

HOH

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Components

#1: Protein 3-5 exonuclease PhoExo I


Mass: 25667.678 Da / Num. of mol.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.9 / Details: PEG 6000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→87.501 Å / Num. all: 74001 / Num. obs: 74001 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 19.41 Å2 / Rpim(I) all: 0.013 / Rrim(I) all: 0.035 / Rsym value: 0.033 / Net I/av σ(I): 14.154 / Net I/σ(I): 30.2 / Num. measured all: 490933
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.52-1.63.10.5361.53029398760.3320.5362.191.1
1.6-1.74.40.3282.445508102880.1730.3284.199.8
1.7-1.826.20.2013.96021896520.0870.2018.1100
1.82-1.9680.126.57245290470.0450.1215.5100
1.96-2.158.10.06511.66764283230.0240.06527.7100
2.15-2.48.10.04516.16119375580.0170.04540.2100
2.4-2.788.10.03320.95405866880.0120.03352.7100
2.78-3.48.10.02324.84595756980.0090.02373.4100
3.4-4.8180.0227.23540744230.0080.0298.1100
4.81-19.6967.40.01826.91820524480.0070.01887.996.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHARPphasing
RefinementResolution: 1.52→19.696 Å / FOM work R set: 0.8774 / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 7019 5.06 %
Rwork0.1597 131687 -
obs0.1607 73987 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.17 Å2 / Biso mean: 33.4 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 1.52→19.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 2 386 3938
Biso mean--22.87 41.35 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073635
X-RAY DIFFRACTIONf_angle_d1.084914
X-RAY DIFFRACTIONf_chiral_restr0.045559
X-RAY DIFFRACTIONf_plane_restr0.005621
X-RAY DIFFRACTIONf_dihedral_angle_d12.7381393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.52-1.53730.3361570.28752843300061
1.5373-1.55530.28531640.26953160332468
1.5553-1.57430.25362000.25833418361875
1.5743-1.59420.2582010.24993767396882
1.5942-1.61520.25871940.23064195438990
1.6152-1.63730.23112410.22454322456394
1.6373-1.66070.24242090.20154434464396
1.6607-1.68550.20532350.19334454468997
1.6855-1.71180.18842710.18844459473097
1.7118-1.73980.20492430.19244523476698
1.7398-1.76980.20352540.17934557481199
1.7698-1.8020.22942580.18164612487099
1.802-1.83660.22892590.169645934852100
1.8366-1.87410.19722710.171845704841100
1.8741-1.91480.20992550.159546094864100
1.9148-1.95930.16922470.157746074854100
1.9593-2.00820.21472100.162146104820100
2.0082-2.06250.19212170.158146744891100
2.0625-2.12310.16332570.149346144871100
2.1231-2.19160.17352450.154546064851100
2.1916-2.26980.16632450.144746214866100
2.2698-2.36050.16182470.155946134860100
2.3605-2.46770.16742470.159345884835100
2.4677-2.59760.19312490.155146354884100
2.5976-2.75990.19282340.161346154849100
2.7599-2.97230.16642840.157745504834100
2.9723-3.27020.20592370.155646284865100
3.2702-3.74060.15712550.146546524907100
3.7406-4.70220.14712080.133846344842100
4.7022-19.69780.15742250.15634524474998
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)
13.3335-1.4850.01515.68690.58230.82810.14690.0357-0.2376-0.111-0.10260.21670.0454-0.0584-0.03040.1237-0.0025-0.00270.15470.01360.11335.8668-37.357614.4396
21.6575-0.14550.82217.4871-0.23193.03450.21140.4082-0.527-0.7967-0.06980.18440.31980.0122-0.09710.224-0.0068-0.08880.2923-0.05150.278929.9985-40.04725.7151
32.82280.47160.64893.3952-0.58473.63120.02020.9404-0.0864-0.73910.0748-0.0120.18230.2111-0.06490.29490.0094-0.01930.3959-0.00560.167934.3126-28.3606-2.5874
42.2527-0.5386-0.28152.14520.16960.9778-0.0256-0.2706-0.38990.1587-0.00450.19860.1668-0.07190.03170.1449-0.01710.00490.17160.04180.169541.425-44.019221.2651
55.04450.03190.18842.3875-0.09640.6246-0.0365-0.3529-0.5650.05310.00550.12590.1033-0.05450.04520.17050.01320.01270.14660.02440.17362.8207-21.626120.8383
62.75070.21510.45563.44940.23243.749-0.0048-0.7181-0.13220.76770.01990.09580.0432-0.16540.040.29530.0130.00790.30920.07010.165613.7487-19.315734.4443
72.598-0.1432-0.15622.06460.22371.07780.00370.2176-0.4358-0.2372-0.09210.20270.1529-0.12950.06880.17880.0001-0.00820.145-0.04290.1935-4.0183-18.353712.9266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 72 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 138 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 227 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 56 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 138 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 139 through 227 )B0

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