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- PDB-6d6k: Structure of polyribonucleotide nucleotidyltransferase from Acine... -

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Basic information

Entry
Database: PDB / ID: 6d6k
TitleStructure of polyribonucleotide nucleotidyltransferase from Acinetobacter baumannii
ComponentsPolyribonucleotide nucleotidyltransferase
KeywordsTRANSFERASE / SSGCID / mRNA degradation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


polyribonucleotide nucleotidyltransferase / polyribonucleotide nucleotidyltransferase activity / mRNA catabolic process / RNA processing / magnesium ion binding / RNA binding / cytoplasm
Similarity search - Function
Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily ...Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily / Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase, RNA-binding domain / Polyribonucleotide nucleotidyltransferase, RNA binding domain / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyribonucleotide nucleotidyltransferase / Polyribonucleotide nucleotidyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of polyribonucleotide nucleotidyltransferase from Acinetobacter baumannii
Authors: Abendroth, J. / Phan, J.N. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyribonucleotide nucleotidyltransferase
B: Polyribonucleotide nucleotidyltransferase


Theoretical massNumber of molelcules
Total (without water)152,7172
Polymers152,7172
Non-polymers00
Water9,080504
1
A: Polyribonucleotide nucleotidyltransferase

A: Polyribonucleotide nucleotidyltransferase

A: Polyribonucleotide nucleotidyltransferase


Theoretical massNumber of molelcules
Total (without water)229,0763
Polymers229,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9500 Å2
ΔGint-33 kcal/mol
Surface area65190 Å2
MethodPISA
2
B: Polyribonucleotide nucleotidyltransferase

B: Polyribonucleotide nucleotidyltransferase

B: Polyribonucleotide nucleotidyltransferase


Theoretical massNumber of molelcules
Total (without water)229,0763
Polymers229,0763
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9220 Å2
ΔGint-31 kcal/mol
Surface area63600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.690, 93.690, 266.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 7 or resid 9...
21(chain B and (resid 2 through 7 or resid 9...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL(chain A and (resid 2 through 7 or resid 9...AA2 - 710 - 15
12LYSLYSILEILE(chain A and (resid 2 through 7 or resid 9...AA9 - 3417 - 42
13METMETLEULEU(chain A and (resid 2 through 7 or resid 9...AA36 - 17844 - 186
14SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
15SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
16SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
17SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
18SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
19SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
110SERSERPROPRO(chain A and (resid 2 through 7 or resid 9...AA2 - 56410 - 572
21SERSERVALVAL(chain B and (resid 2 through 7 or resid 9...BB2 - 710 - 15
22LYSLYSILEILE(chain B and (resid 2 through 7 or resid 9...BB9 - 3417 - 42
23METMETGLNGLN(chain B and (resid 2 through 7 or resid 9...BB36 - 5544 - 63
24SERSERGLUGLU(chain B and (resid 2 through 7 or resid 9...BB2 - 55810 - 566
25SERSERGLUGLU(chain B and (resid 2 through 7 or resid 9...BB2 - 55810 - 566
26SERSERGLUGLU(chain B and (resid 2 through 7 or resid 9...BB2 - 55810 - 566
27SERSERGLUGLU(chain B and (resid 2 through 7 or resid 9...BB2 - 55810 - 566

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Components

#1: Protein Polyribonucleotide nucleotidyltransferase / Polynucleotide phosphorylase / PNPase


Mass: 76358.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: pnp, A388_03473, A7A65_13105, A7M79_05700, A7M90_01190, A7N09_01970, AB895_1857, ABUW_3518, APD06_02100, AZE33_01855, B4R90_00995, B9X95_14475, BGC29_15530, BWP00_17325, CAS83_01330, CBE85_ ...Gene: pnp, A388_03473, A7A65_13105, A7M79_05700, A7M90_01190, A7N09_01970, AB895_1857, ABUW_3518, APD06_02100, AZE33_01855, B4R90_00995, B9X95_14475, BGC29_15530, BWP00_17325, CAS83_01330, CBE85_05335, CBI29_00441, CEJ63_09865, CHQ89_05525, CPI82_06995, CUC62_01320, CV949_02160, CV950_09585, CV951_02090, CV952_02080, IX87_16365, LV38_00189
Plasmid: AcbaC.17868.b.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: V5VH92, UniProt: B0VLR7*PLUS, polyribonucleotide nucleotidyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.21 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, C9: 32% PEG 4000, 800mM LiCl, 100mM Tris Base / HCl: AcbaC.17868.b.B1.PS38264 at 20.7mg/ml: cryo: direct: tray 292329c9: puck vqb8-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2018
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→44.435 Å / Num. obs: 45569 / % possible obs: 99.8 % / Redundancy: 6.445 % / Biso Wilson estimate: 36.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Χ2: 1.043 / Net I/σ(I): 20.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.576.4860.5054.2933550.9170.55199.8
2.57-2.646.4210.415.2832940.9410.44899.9
2.64-2.716.4930.3446.0831800.9570.37799.9
2.71-2.86.4550.2667.6331000.9710.29199.9
2.8-2.896.4770.2169.2130210.9830.23699.8
2.89-2.996.4540.18110.7628960.9860.19899.9
2.99-3.16.4550.14113.5528030.9910.15599.9
3.1-3.236.4220.10816.6927210.9940.119100
3.23-3.376.4780.08520.6925800.9950.09399.8
3.37-3.546.4790.0724.324680.9970.07699.8
3.54-3.736.3950.05827.9823450.9980.06499.5
3.73-3.956.4570.05131.1922290.9980.05599.7
3.95-4.236.430.04534.1520930.9980.0599.8
4.23-4.566.430.03839.5119500.9990.04299.7
4.56-56.4320.03740.7817990.9990.0499.9
5-5.596.4480.03739.7116300.9990.04199.8
5.59-6.466.4410.03839.3214220.9980.04299.6
6.46-7.916.4050.0314312340.9990.034100
7.91-11.186.3780.02351.9693910.02599.8
11.18-44.4356.0590.02350.2751010.02592.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3092)refinement
PDB_EXTRACTdata extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3gme per morda

3gme


Resolution: 2.5→44.435 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.54
RfactorNum. reflection% reflection
Rfree0.2072 2017 4.43 %
Rwork0.1569 --
obs0.1592 45495 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.9 Å2 / Biso mean: 46.7395 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 2.5→44.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8085 0 0 505 8590
Biso mean---44.41 -
Num. residues----1095
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4817X-RAY DIFFRACTION8.135TORSIONAL
12B4817X-RAY DIFFRACTION8.135TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56250.2561660.190830523218100
2.5625-2.63180.24011410.175831223263100
2.6318-2.70930.23931480.172831003248100
2.7093-2.79670.2451300.172631153245100
2.7967-2.89660.25421650.171130853250100
2.8966-3.01260.2571140.187231623276100
3.0126-3.14960.24871200.194231033223100
3.1496-3.31570.24171380.179531333271100
3.3157-3.52330.2021590.168330783237100
3.5233-3.79520.19861460.150530843230100
3.7952-4.17690.18551310.136331323263100
4.1769-4.78070.16941630.116531063269100
4.7807-6.02080.18441550.142830993254100
6.0208-44.4420.1891410.1563107324898
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)
11.47610.1446-0.09622.5458-0.21080.9981-0.0190.0378-0.0244-0.18580.11210.18960.0592-0.1945-0.07490.1841-0.0157-0.01260.27030.01240.2735-28.195850.4505-3.2575
23.57820.0514-0.86993.2783-1.14543.72290.35610.4337-0.1749-0.7718-0.2333-0.9295-0.76990.5107-0.12260.9143-0.04070.10670.7139-0.12950.6789-13.51131.3788-27.6743
32.1175-0.07990.89210.76890.02072.55920.0276-0.1869-0.1306-0.04220.05320.11830.0489-0.2099-0.08360.2923-0.0240.01740.2020.02930.327-14.974628.50543.2759
42.13710.60680.35081.6901-0.07631.29420.09370.0111-0.26850.0471-0.0162-0.11880.22210.0957-0.0930.28810.0591-0.01010.207-0.01930.288812.366228.056958.5616
51.47220.1056-0.12020.6089-0.39321.5342-0.0668-0.729-0.12570.41090.0240.1236-0.1421-0.03630.0690.5141-0.033-0.01050.49880.00960.2953-12.859226.609179.7955
61.3905-0.40190.45771.2719-0.45752.11410.12360.0838-0.129-0.0682-0.01860.01530.20520.044-0.11810.2948-0.0528-0.03060.2525-0.02740.3375-12.52627.885654.0586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 263 )A2 - 263
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 312 )A264 - 312
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 564 )A313 - 564
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 226 )B2 - 226
5X-RAY DIFFRACTION5chain 'B' and (resid 227 through 349 )B227 - 349
6X-RAY DIFFRACTION6chain 'B' and (resid 350 through 558 )B350 - 558

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