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- PDB-6l19: The crystal structure of competence or damage-inducible protein f... -

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Basic information

Entry
Database: PDB / ID: 6l19
TitleThe crystal structure of competence or damage-inducible protein from Enterobacter asburiae
ComponentsPncC family amidohydrolase
KeywordsHYDROLASE / competence or damage-inducible protein / ComA / Enterobacter asburiae
Function / homologyCinA-like / CinA, C-terminal / CinA-like, C-terminal / Competence-damaged protein / Maf protein / hydrolase activity / Alpha-Beta Complex / Alpha Beta / PncC family amidohydrolase
Function and homology information
Biological speciesEnterobacter asburiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsWang, L. / Chen, Y. / Liu, W. / Lan, J. / Shang, F. / Xu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31200556 China
National Natural Science Foundation of China21272031 China
CitationJournal: To Be Published
Title: The crystal structure of Competence or damage-inducible protein from Enterobacter asburiae
Authors: Wang, L. / Chen, Y. / Liu, W. / Lan, J. / Shang, F. / Xu, Y.
History
DepositionSep 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PncC family amidohydrolase
B: PncC family amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7586
Polymers36,5852
Non-polymers1744
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-40 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.915, 128.915, 56.277
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein PncC family amidohydrolase


Mass: 18292.352 Da / Num. of mol.: 2 / Mutation: T68M, Q137E, V141M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter asburiae (bacteria) / Gene: DFS27_0727 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A495LDQ0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.5 M Ammonium phosphate monobasic, 0.1 M Tric-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 27236 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 27.34 Å2 / Rsym value: 0.142 / Net I/σ(I): 21.6
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 790 / Rsym value: 0.917 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→32.23 Å / SU ML: 0.1927 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.4917
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 1980 7.37 %
Rwork0.1848 24880 -
obs0.1875 26860 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.31 Å2
Refinement stepCycle: LAST / Resolution: 2.13→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 9 214 2612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872457
X-RAY DIFFRACTIONf_angle_d0.88283332
X-RAY DIFFRACTIONf_chiral_restr0.0516402
X-RAY DIFFRACTIONf_plane_restr0.0041436
X-RAY DIFFRACTIONf_dihedral_angle_d7.5761996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.26021310.2191663X-RAY DIFFRACTION94.07
2.18-2.240.26211340.20761725X-RAY DIFFRACTION97.38
2.24-2.310.23381370.18741716X-RAY DIFFRACTION97.27
2.31-2.380.21271380.18461745X-RAY DIFFRACTION98.38
2.38-2.460.23551410.18581755X-RAY DIFFRACTION98.49
2.46-2.560.23731410.18961750X-RAY DIFFRACTION98.8
2.56-2.680.26131410.19151747X-RAY DIFFRACTION98.85
2.68-2.820.2411410.19531788X-RAY DIFFRACTION99.54
2.82-30.26081430.19061778X-RAY DIFFRACTION99.53
3-3.230.21871420.1951783X-RAY DIFFRACTION99.69
3.23-3.550.23571450.18531815X-RAY DIFFRACTION99.85
3.55-4.070.18511440.17021824X-RAY DIFFRACTION100
4.07-5.120.1841470.15181837X-RAY DIFFRACTION99.95
5.12-32.230.21851550.20411954X-RAY DIFFRACTION99.58

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