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- PDB-7uda: Structure of the EstG -

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Basic information

Entry
Database: PDB / ID: 7uda
TitleStructure of the EstG
ComponentsBeta-lactamase domain-containing protein
KeywordsHYDROLASE / alpha/beta fold
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / Beta-lactamase-related domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsChen, Z. / Gabelli, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R35GM136221 United States
CitationJournal: Curr.Biol. / Year: 2023
Title: EstG is a novel esterase required for cell envelope integrity in Caulobacter.
Authors: Daitch, A.K. / Orsburn, B.C. / Chen, Z. / Alvarez, L. / Eberhard, C.D. / Sundararajan, K. / Zeinert, R. / Kreitler, D.F. / Jakoncic, J. / Chien, P. / Cava, F. / Gabelli, S.B. / Goley, E.D.
History
DepositionMar 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 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: Beta-lactamase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4396
Polymers49,2251
Non-polymers2145
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.321, 110.321, 55.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Beta-lactamase domain-containing protein


Mass: 49224.500 Da / Num. of mol.: 1
Fragment: estG, Esterase for Stress Tolerance acting on glucans
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Plasmid: pEG1622 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9A800
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.46 Å3/Da / Density % sol: 64.41 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG500 MME, 10% PEG20000, 0.1 M Tris/Bicine pH 8.5 and 90 mM mixture of sodium nitrate, sodium phosphate dibasic and ammonium sulfate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.47→29.62 Å / Num. obs: 24085 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.5 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.47-2.570.7811634525150.7550.3240.8472.491.9
8.92-29.60.04736105540.9950.020.05226.397.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ci8

1ci8


Resolution: 2.47→29.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2159 / WRfactor Rwork: 0.1752 / FOM work R set: 0.8406 / SU B: 6.945 / SU ML: 0.154 / SU R Cruickshank DPI: 0.2452 / SU Rfree: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1171 4.9 %RANDOM
Rwork0.18 ---
obs0.182 22895 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 187.25 Å2 / Biso mean: 52.356 Å2 / Biso min: 23.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0 Å2
2---0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2.47→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 12 31 3061
Biso mean--48.75 43.13 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133121
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172982
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6464241
X-RAY DIFFRACTIONr_angle_other_deg1.2861.5756864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2921.242153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24715488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6581524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
LS refinement shellResolution: 2.474→2.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 73 -
Rwork0.273 1470 -
all-1543 -
obs--87.62 %

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