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- PDB-7u1c: Structure of EstG crystalized with SO4 and Tris -

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Basic information

Entry
Database: PDB / ID: 7u1c
TitleStructure of EstG crystalized with SO4 and Tris
ComponentsBeta-lactamase domain-containing protein
KeywordsHYDROLASE / CCNA_01638 / alpha/beta fold / EstG / beta-lactamase binding protein
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: 2.09 Å
AuthorsGabelli, S.B. / Chen, Z.
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)50,1644
Polymers49,9221
Non-polymers2413
Water5,152286
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)111.253, 111.253, 56.872
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: 49922.344 Da / Num. of mol.: 1
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 pLYS / References: UniProt: Q9A800
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.53 Å3/Da / Density % sol: 65.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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 / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92012 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: 0.92012 Å / Relative weight: 1
ReflectionResolution: 2.09→28.44 Å / Num. obs: 41361 / % possible obs: 99.2 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.037 / Rrim(I) all: 0.099 / Net I/σ(I): 12.4 / Num. measured all: 288425 / Scaling rejects: 24
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
2.09-2.146.80.8291959629000.7670.3390.8972.690.3
9.1-28.446.70.04935755350.9970.020.05330.897

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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: 2.09→27.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.565 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2098 2092 5.1 %RANDOM
Rwork0.1717 ---
obs0.1736 39246 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.73 Å2 / Biso mean: 43.569 Å2 / Biso min: 23.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.09→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 14 286 3317
Biso mean--37.35 57.11 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133107
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172979
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.6454222
X-RAY DIFFRACTIONr_angle_other_deg1.381.5756851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1175400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.56421.2150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3411524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023542
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02702
LS refinement shellResolution: 2.09→2.141 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.266 170 -
Rwork0.243 2541 -
obs--89.59 %

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