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- PDB-7u1b: Crystal structure of EstG in complex with tantalum cluster -

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Basic information

Entry
Database: PDB / ID: 7u1b
TitleCrystal structure of EstG in complex with tantalum cluster
ComponentsBeta-lactamase domain-containing protein
KeywordsHYDROLASE / alpha/beta fold / CCNA_01638
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / HEXATANTALUM DODECABROMIDE / Beta-lactamase-related domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsChen, Z. / Gabelli, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 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
DepositionFeb 20, 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)52,3485
Polymers49,9221
Non-polymers2,4264
Water18010
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)111.765, 111.765, 57.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase domain-containing protein


Mass: 49922.344 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) / Strain: ATCC 19089 / CB15 / Gene: CC_1567 / Plasmid: pEG1622 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9A800

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Non-polymers , 5 types, 14 molecules

#2: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br12Ta6
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.64 Å3/Da / Density % sol: 66.21 % / 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: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.62→28.71 Å / Num. obs: 21379 / % possible obs: 99.5 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.037 / Rrim(I) all: 0.113 / Net I/σ(I): 16.9 / Num. measured all: 195511
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.62-2.758.30.762274227410.7980.2780.8113.196.9
8.71-28.718.70.0454366250.9990.0140.04247.297.4

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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: 2.62→27.96 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2133 / WRfactor Rwork: 0.1755 / FOM work R set: 0.8299 / SU B: 8.745 / SU ML: 0.177 / SU R Cruickshank DPI: 0.3214 / SU Rfree: 0.2455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2336 1150 5.4 %RANDOM
Rwork0.1896 ---
obs0.1919 20214 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 420.63 Å2 / Biso mean: 49.622 Å2 / Biso min: 25.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å20 Å2
2--0.49 Å20 Å2
3----0.98 Å2
Refinement stepCycle: final / Resolution: 2.62→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 42 10 3084
Biso mean--195.63 40.86 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133187
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173017
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.7014457
X-RAY DIFFRACTIONr_angle_other_deg1.2691.5766940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5855405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03521.258151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.251524
X-RAY DIFFRACTIONr_chiral_restr0.0750.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023585
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02707
LS refinement shellResolution: 2.625→2.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 77 -
Rwork0.28 1394 -
all-1471 -
obs--94.48 %

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