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- PDB-5v8c: LytR-Csp2A-Psr enzyme from Actinomyces oris -

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Basic information

Entry
Database: PDB / ID: 5v8c
TitleLytR-Csp2A-Psr enzyme from Actinomyces oris
ComponentsTranscriptional regulator
KeywordsTRANSCRIPTION / LCP / LytR-Cps2A-Psr / protein glycosylation / Gram positive surface glycosylation
Function / homologyCell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / membrane => GO:0016020 / : / PHOSPHATE ION / Transcriptional regulator
Function and homology information
Biological speciesActinomyces oris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsAmer, B.R. / Sawaya, M.R. / Liauw, B. / Fu, J.Y. / Ton-That, H. / Clubb, R.T.
CitationJournal: MBio / Year: 2019
Title: Structure and Mechanism of LcpA, a Phosphotransferase That Mediates Glycosylation of a Gram-Positive Bacterial Cell Wall-Anchored Protein.
Authors: Siegel, S.D. / Amer, B.R. / Wu, C. / Sawaya, M.R. / Gosschalk, J.E. / Clubb, R.T. / Ton-That, H.
History
DepositionMar 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4734
Polymers30,9651
Non-polymers5083
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.850, 69.070, 82.010
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 Transcriptional regulator


Mass: 30964.828 Da / Num. of mol.: 1 / Fragment: UNP residues 71-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomyces oris (bacteria) / Gene: AXE84_08820 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0X8K2V1
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.87 Å3/Da / Density % sol: 34.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate pH 5.5, 25% PEG4000, 20% 2-propanol, 5 mM DTT, 200 mM NaCl, 5 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.51→52.83 Å / Num. obs: 8332 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.354 % / Biso Wilson estimate: 89.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.056 / Χ2: 0.997 / Net I/σ(I): 16.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.51-2.576.3091.0141.585720.7561.10593.5
2.57-2.646.6780.8572.065740.8820.929100
2.64-2.726.3650.6882.485870.9090.74999.8
2.72-2.86.3020.5363.45500.9470.58599.1
2.8-2.896.3690.4024.475420.9520.43799.4
2.89-2.996.8130.2676.685250.9830.28999.6
2.99-3.116.6350.1789.625130.9920.193100
3.11-3.236.5020.12412.064860.9960.135100
3.23-3.386.2840.09515.914900.9980.10399.8
3.38-3.546.0570.08118.514380.9950.08897.6
3.54-3.736.5050.06123.444360.9970.06699.8
3.73-3.966.5250.05527.24130.9980.06100
3.96-4.236.2930.04729.293930.9980.052100
4.23-4.575.9580.04333.33570.9980.04897.3
4.57-5.016.5610.03936.443350.9990.042100
5.01-5.66.3180.0435.693080.9980.044100
5.6-6.475.9240.0435.752750.9980.044100
6.47-7.925.8330.03737.762340.9980.04196.7
7.92-11.25.8650.04239.071920.9980.04699
11.2-52.835.1520.04537.041120.9970.0594.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.51→52.83 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 1.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.418 / SU Rfree Blow DPI: 0.333 / SU Rfree Cruickshank DPI: 0.335
RfactorNum. reflection% reflectionSelection details
Rfree0.272 416 5.01 %RANDOM
Rwork0.221 ---
obs0.223 8302 99.1 %-
Displacement parametersBiso max: 188.51 Å2 / Biso mean: 98.01 Å2 / Biso min: 63.88 Å2
Baniso -1Baniso -2Baniso -3
1--18.845 Å20 Å20 Å2
2---0.049 Å20 Å2
3---18.894 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.51→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1954 0 30 6 1990
Biso mean--119.89 79.28 -
Num. residues----272
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d683SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2017HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion295SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2278SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2017HARMONIC30.007
X-RAY DIFFRACTIONt_angle_deg2751HARMONIC30.93
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion21.23
LS refinement shellResolution: 2.51→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3066 115 5.03 %
Rwork0.2528 2171 -
all0.2554 2286 -
obs--98.58 %
Refinement TLS params.Method: refined / Origin x: 10.6784 Å / Origin y: 4.3011 Å / Origin z: 7.7936 Å
111213212223313233
T-0.0869 Å20.0095 Å20.0089 Å2--0.0449 Å2-0.0058 Å2---0.1204 Å2
L1.2799 °2-0.217 °2-0.06 °2-1.308 °2-0.9087 °2--4.051 °2
S-0.126 Å °0.1342 Å °0.0381 Å °0.1384 Å °0.0696 Å °0.0016 Å °0.6926 Å °0.2548 Å °0.0564 Å °
Refinement TLS groupSelection details: { A|78 - A|368 }

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