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- PDB-5tzb: Burkholderia sp. beta-aminopeptidase -

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Basic information

Entry
Database: PDB / ID: 5tzb
TitleBurkholderia sp. beta-aminopeptidase
ComponentsD-aminopeptidase
KeywordsHYDROLASE / beta-aminopeptidase / enzyme / Burkholderia / Ntn hydrolases / beta-amino acids
Function / homologyL-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / 4-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBurkholderia sp. LK4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.977 Å
AuthorsMcGowan, S. / Drinkwater, N. / John, M. / Dumsday, G.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of a beta-aminopeptidase from an Australian Burkholderia sp.
Authors: John-White, M. / Dumsday, G.J. / Johanesen, P. / Lyras, D. / Drinkwater, N. / McGowan, S.
History
DepositionNov 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: D-aminopeptidase
B: D-aminopeptidase
C: D-aminopeptidase
G: D-aminopeptidase
E: D-aminopeptidase
F: D-aminopeptidase
D: D-aminopeptidase
H: D-aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,86412
Polymers320,7048
Non-polymers1604
Water32,1031782
1
A: D-aminopeptidase
B: D-aminopeptidase
C: D-aminopeptidase
D: D-aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,4326
Polymers160,3524
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17650 Å2
ΔGint-46 kcal/mol
Surface area39000 Å2
MethodPISA
2
G: D-aminopeptidase
E: D-aminopeptidase
F: D-aminopeptidase
H: D-aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,4326
Polymers160,3524
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17750 Å2
ΔGint-46 kcal/mol
Surface area38800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.451, 133.260, 117.068
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-aminopeptidase


Mass: 40087.938 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. LK4 (bacteria) / Gene: VK92_01140 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS DE3 / References: UniProt: A0A0J6Q6M7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1782 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 35 % 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 7.0 and 5 % PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 10, 2015
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.98→45.711 Å / Num. obs: 190171 / % possible obs: 97.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.5 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.98-2.013.80.9240.591187.1
10.83-62.713.70.0450.916198.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B65

1b65


Resolution: 1.977→45.711 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 9243 4.99 %
Rwork0.1979 --
obs0.1999 185395 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.977→45.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20361 0 4 1782 22147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720755
X-RAY DIFFRACTIONf_angle_d1.05628286
X-RAY DIFFRACTIONf_dihedral_angle_d11.6327190
X-RAY DIFFRACTIONf_chiral_restr0.0443257
X-RAY DIFFRACTIONf_plane_restr0.0063777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.977-1.99950.31352440.26595209X-RAY DIFFRACTION84
1.9995-2.0230.27013210.26055838X-RAY DIFFRACTION95
2.023-2.04770.30663290.24965974X-RAY DIFFRACTION97
2.0477-2.07360.27662920.24736012X-RAY DIFFRACTION97
2.0736-2.10090.29632970.24755964X-RAY DIFFRACTION97
2.1009-2.12960.27662750.23856078X-RAY DIFFRACTION97
2.1296-2.16010.29333280.23765967X-RAY DIFFRACTION97
2.1601-2.19230.27673450.2395981X-RAY DIFFRACTION97
2.1923-2.22660.46972740.43385034X-RAY DIFFRACTION82
2.2266-2.26310.63012090.6323978X-RAY DIFFRACTION64
2.2631-2.30210.54272410.39084505X-RAY DIFFRACTION73
2.3021-2.3440.25793280.20776048X-RAY DIFFRACTION98
2.344-2.3890.25793280.19575991X-RAY DIFFRACTION98
2.389-2.43780.22653470.18475968X-RAY DIFFRACTION98
2.4378-2.49080.22813230.19366041X-RAY DIFFRACTION98
2.4908-2.54870.25043320.19376052X-RAY DIFFRACTION98
2.5487-2.61250.24823080.18216085X-RAY DIFFRACTION98
2.6125-2.68310.23863330.18146010X-RAY DIFFRACTION98
2.6831-2.7620.22433140.18246069X-RAY DIFFRACTION98
2.762-2.85120.22673320.17846061X-RAY DIFFRACTION98
2.8512-2.95310.22313080.17826122X-RAY DIFFRACTION98
2.9531-3.07130.2252900.17656064X-RAY DIFFRACTION98
3.0713-3.2110.2213160.17526089X-RAY DIFFRACTION98
3.211-3.38030.21513200.17376141X-RAY DIFFRACTION99
3.3803-3.5920.21753200.16916116X-RAY DIFFRACTION99
3.592-3.86920.22113160.20466069X-RAY DIFFRACTION98
3.8692-4.25830.17563240.14826080X-RAY DIFFRACTION98
4.2583-4.87390.1482760.11666240X-RAY DIFFRACTION99
4.8739-6.13820.15453040.12256187X-RAY DIFFRACTION99
6.1382-45.72340.15373690.1316179X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 23.6775 Å / Origin y: -38.2948 Å / Origin z: 13.3942 Å
111213212223313233
T0.1187 Å2-0.0238 Å2-0.0023 Å2-0.0973 Å2-0.0131 Å2--0.1786 Å2
L0.3119 °2-0.0297 °2-0.0778 °2-0.0897 °20.0049 °2--0.8197 °2
S-0.0034 Å °0.1023 Å °-0.0486 Å °-0.0147 Å °0.0106 Å °0.0138 Å °-0.0123 Å °-0.0865 Å °-0.0106 Å °
Refinement TLS groupSelection details: ALL

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