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- PDB-6lna: YdiU complex with AMPNPP and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 6lna
TitleYdiU complex with AMPNPP and Mn2+
ComponentsProtein adenylyltransferase SelO
KeywordsTRANSFERASE / ComPlex
Function / homology
Function and homology information


AMPylase activity / protein adenylylation / protein adenylyltransferase / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / magnesium ion binding / ATP binding
Similarity search - Function
: / Protein adenylyltransferase SelO / Protein adenylyltransferase SelO
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Protein adenylyltransferase SelO / Protein nucleotidyltransferase SelO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsLi, B. / Yang, Y. / Ma, Y.
CitationJournal: Cell Rep / Year: 2020
Title: The YdiU Domain Modulates Bacterial Stress Signaling through Mn 2+ -Dependent UMPylation.
Authors: Yang, Y. / Yue, Y. / Song, N. / Li, C. / Yuan, Z. / Wang, Y. / Ma, Y. / Li, H. / Zhang, F. / Wang, W. / Jia, H. / Li, P. / Li, X. / Wang, Q. / Ding, Z. / Dong, H. / Gu, L. / Li, B.
History
DepositionDec 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein adenylyltransferase SelO
B: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,27210
Polymers108,9602
Non-polymers1,3128
Water29,9411662
1
A: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1365
Polymers54,4801
Non-polymers6564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-6 kcal/mol
Surface area19130 Å2
MethodPISA
2
B: Protein adenylyltransferase SelO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1365
Polymers54,4801
Non-polymers6564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-5 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.430, 73.541, 122.649
Angle α, β, γ (deg.)90.000, 102.490, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

21A-855-

HOH

31A-1042-

HOH

41B-816-

HOH

51B-1154-

HOH

61B-1315-

HOH

71B-1356-

HOH

81B-1413-

HOH

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Components

#1: Protein Protein adenylyltransferase SelO


Mass: 54480.004 Da / Num. of mol.: 2 / Mutation: C272S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ydiU, selO, BMT91_02235, BvCmsHHP001_02698, CI694_12210, DAH34_03285, E2127_19880, E2129_01950, EXX71_03705, FORC82_2205, FWK02_14790, NCTC9073_05692, PGD_01529, SAMEA3472080_01323
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A024L327, UniProt: P77649*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1662 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG8000 0.2M calcium acetate PH6.5 0.1M Sodium cacodylate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2019
RadiationMonochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→27.442 Å / Num. obs: 97925 / % possible obs: 91.5 % / Redundancy: 15.1 % / CC1/2: 0.991 / Rpim(I) all: 0.053 / Rrim(I) all: 0.094 / Net I/σ(I): 12.3
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 5.3 / Num. unique obs: 97925 / CC1/2: 0.845 / Rpim(I) all: 0.221 / Rrim(I) all: 0.397 / Χ2: 0.42 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6III

6iii


Resolution: 1.701→27.442 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.11
RfactorNum. reflection% reflection
Rfree0.1857 4983 5.09 %
Rwork0.1402 --
obs0.1426 97848 91.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.36 Å2 / Biso mean: 12.3081 Å2 / Biso min: 1.59 Å2
Refinement stepCycle: final / Resolution: 1.701→27.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7463 0 68 1662 9193
Biso mean--5.91 22.38 -
Num. residues----927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.701-1.72030.16471550.1167321495
1.7203-1.74060.19611620.1315336799
1.7406-1.76180.18651600.1362335399
1.7618-1.78410.1951930.1371332499
1.7841-1.80760.21691670.1417336499
1.8076-1.83230.20391840.1502339299
1.8323-1.85850.20871650.1468329899
1.8585-1.88620.24221650.1511336899
1.8862-1.91570.2033930.1595168350
1.9157-1.94710.21921260.1558198860
1.9471-1.98060.181830.1352335099
1.9806-2.01670.20721880.139329999
2.0167-2.05540.20171650.1394335299
2.0554-2.09740.2031910.1438330899
2.0974-2.1430.1751640.1382332799
2.143-2.19280.19531720.1362331798
2.1928-2.24760.1841000.1488201559
2.2476-2.30830.22051090.1464205461
2.3083-2.37620.18231880.139333199
2.3762-2.45290.18641940.1429332198
2.4529-2.54050.18481770.14334599
2.5405-2.64210.17491800.1417330898
2.6421-2.76230.18661970.1398330398
2.7623-2.90770.18031840.1419332898
2.9077-3.08970.20191780.1454334298
3.0897-3.32790.17682010.142328297
3.3279-3.66210.16821500.1329284283
3.6621-4.19040.15271320.1261253974
4.1904-5.27330.15941700.1266329395
5.2733-60.18031900.1626325893

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