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- PDB-6rk6: Characterization of an intertidal zone metagenome oligoribonuclea... -

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Basic information

Entry
Database: PDB / ID: 6rk6
TitleCharacterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity.
ComponentsOligoribonuclease
KeywordsHYDROLASE / oligoribonuclease / metagenome / RNA / homodimer
Function / homologyRibonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsPiotrowski, Y. / Berg, K. / Klebl, D.P. / Leiros, I. / Larsen, A.N.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway Norway
CitationJournal: Febs Open Bio / Year: 2019
Title: Characterization of an intertidal zone metagenome oligoribonuclease and the role of the intermolecular disulfide bond for homodimer formation and nuclease activity.
Authors: Piotrowski, Y. / Berg, K. / Klebl, D.P. / Leiros, I. / Larsen, A.N.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 24, 2024Group: 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 1.5Nov 6, 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: Oligoribonuclease
B: Oligoribonuclease
C: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8206
Polymers64,6553
Non-polymers1653
Water00
1
A: Oligoribonuclease
C: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2134
Polymers43,1032
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-29 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: Oligoribonuclease
hetero molecules

B: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2134
Polymers43,1032
Non-polymers1102
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_345-x-2,-x+y-1,-z+1/31
Buried area3100 Å2
ΔGint-31 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.322, 108.322, 101.334
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Oligoribonuclease


Mass: 21551.566 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Gene: orn / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta 2 / References: EC: 3.1.13.3
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Hepes, pH 7.0, 5% (v/v) PEG 8000. / PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016 / Details: Focussing mirror
RadiationMonochromator: Si111 single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.15→44.58 Å / Num. obs: 12264 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 79.0105713424 Å2 / Rpim(I) all: 0.076 / Net I/σ(I): 8.2
Reflection shellResolution: 3.15→3.37 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2200 / Rpim(I) all: 0.551 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBZ

2gbz


Resolution: 3.15→44.58 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.33
RfactorNum. reflection% reflection
Rfree0.2655 926 7.57 %
Rwork0.2452 --
obs0.2467 12228 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 3 0 4379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034461
X-RAY DIFFRACTIONf_angle_d0.6786031
X-RAY DIFFRACTIONf_dihedral_angle_d10.5872729
X-RAY DIFFRACTIONf_chiral_restr0.043676
X-RAY DIFFRACTIONf_plane_restr0.004770
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1501-3.31610.35971560.361554X-RAY DIFFRACTION100
3.3161-3.52380.34321440.31951588X-RAY DIFFRACTION100
3.5238-3.79570.30141290.28721579X-RAY DIFFRACTION100
3.7957-4.17750.27021510.25011599X-RAY DIFFRACTION100
4.1775-4.78140.21411220.21531629X-RAY DIFFRACTION100
4.7814-6.02170.27251080.22391641X-RAY DIFFRACTION100
6.0217-44.58470.22241160.21131712X-RAY DIFFRACTION99
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)
14.0869-1.7646-0.84520.8797-0.15554.38740.39460.2906-0.35840.3569-0.26950.28091.120.1632-0.08480.8646-0.02070.06290.47060.0370.6295-60.809814.99869.9456
24.2433-0.49471.25992.5841-1.79534.6230.02640.19680.3174-0.3642-0.2125-0.29480.33320.48020.12850.65990.07080.10710.6251-0.1130.7182-54.046316.527710.2349
3-0.07110.14970.06837.4621-1.73884.2896-0.0382-0.6309-0.21661.07620.15970.20830.0597-0.2339-0.15290.6909-0.0980.11090.7456-0.06490.56-75.632919.030617.3481
43.722-0.4297-0.15424.42371.30164.3859-0.0557-0.07030.3254-0.35510.30790.3505-0.29750.7903-0.18270.5844-0.21420.05730.8924-0.16710.791-93.5522.743816.5879
51.68321.00351.28971.708-0.12223.6391-0.0242-0.87860.24460.25920.1816-0.46310.16860.570.06480.62820.1642-0.10820.9699-0.10450.6974-89.7459-16.671123.31
60.46620.9220.35122.9509-1.11835.42510.2962-0.09350.39310.2731-0.26360.6156-0.8876-0.10160.06750.67890.06350.02270.5333-0.11140.598-66.643543.539910.8711
75.23754.89052.8425.30610.66717.1664-0.16490.3299-0.3531-0.6135-0.155-0.4338-1.20710.35750.46230.88320.0222-0.11510.4806-0.01490.6715-54.841249.4258-1.7044
82.83751.96091.50846.6454-0.43013.0505-0.1901-0.7948-0.24210.0792-0.1993-0.1349-0.7729-0.11940.3670.7213-0.00420.01180.6437-0.05250.5822-65.730138.401915.2088
90.1678-0.56890.38652.3209-1.96082.01080.05890.4476-0.3225-0.33650.3797-0.63040.2702-0.7167-0.56161.15210.10680.01130.7657-0.0330.8511-80.196336.7402-1.8976
104.43126.1426-2.16948.5672-2.47724.95590.03661.26730.4910.20270.67641.7620.114-1.1357-0.88660.57490.009-0.21730.86180.05910.7082-81.036636.69227.79
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 130 )
3X-RAY DIFFRACTION3chain 'A' and (resid 131 through 181 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 130 )
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 181 )
6X-RAY DIFFRACTION6chain 'C' and (resid 5 through 47 )
7X-RAY DIFFRACTION7chain 'C' and (resid 48 through 81 )
8X-RAY DIFFRACTION8chain 'C' and (resid 82 through 144 )
9X-RAY DIFFRACTION9chain 'C' and (resid 145 through 159 )
10X-RAY DIFFRACTION10chain 'C' and (resid 160 through 182 )

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