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- PDB-5gkv: Crystal Structure of a Novel Penicillin-Binding Protein (PBP) Hom... -

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Basic information

Entry
Database: PDB / ID: 5gkv
TitleCrystal Structure of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus
ComponentsEsterase A
KeywordsHYDROLASE / Penicillin-binding protein / biochemical assay
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / Esterase A
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.901 Å
AuthorsNgo, T.D. / Ryu, B.H. / Kim, B.Y. / Yoo, W.K. / Lee, E.J. / Lee, S.J. / Kim, T.D. / Kim, K.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2013K2A1A2053659 Korea, Republic Of
CitationJournal: To Be Published
Title: Biochemical and Structural Analysis of a Novel Penicillin-Binding Protein (PBP) Homolog from Caulobacter crescentus
Authors: Ryu, B.H. / Ngo, T.D. / Kim, B.Y. / Yoo, W.K. / Lee, E.J. / Lee, S.J. / Kim, K.K. / Kim, T.D.
History
DepositionJul 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Esterase A


Theoretical massNumber of molelcules
Total (without water)41,3451
Polymers41,3451
Non-polymers00
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13570 Å2
Unit cell
Length a, b, c (Å)58.277, 67.308, 92.093
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 Esterase A


Mass: 41345.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: CC_0255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ABH2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 295 K / Method: microbatch
Details: 50mM potassium phosphate monobasic, 20%(w/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.919805 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919805 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29140 / % possible obs: 99.99 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 34.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYT

3zyt


Resolution: 1.901→29.144 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.201 1987 6.87 %
Rwork0.1704 --
obs0.1726 28932 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.48 Å2 / Biso mean: 24.572 Å2 / Biso min: 10.93 Å2
Refinement stepCycle: final / Resolution: 1.901→29.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 0 319 3117
Biso mean---32.16 -
Num. residues----371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072875
X-RAY DIFFRACTIONf_angle_d0.8573914
X-RAY DIFFRACTIONf_chiral_restr0.057418
X-RAY DIFFRACTIONf_plane_restr0.007522
X-RAY DIFFRACTIONf_dihedral_angle_d12.6171682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9007-1.94830.21961340.18181866200097
1.9483-2.00090.21661390.16181844198398
2.0009-2.05980.20871390.16811894203399
2.0598-2.12620.19721420.16051912205499
2.1262-2.20220.20621410.16251900204199
2.2022-2.29040.22481380.17741870200898
2.2904-2.39450.23661420.17031913205599
2.3945-2.52070.23071420.177519232065100
2.5207-2.67860.24331410.186719282069100
2.6786-2.88520.22381430.185219362079100
2.8852-3.17520.23011440.192519562100100
3.1752-3.6340.18441420.17471947208999
3.634-4.57550.16161470.144919802127100
4.5755-29.1470.17741530.167820762229100

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