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- PDB-3nfb: Crystal structure of the N-terminal beta-aminopeptidase BapA in c... -

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Basic information

Entry
Database: PDB / ID: 3nfb
TitleCrystal structure of the N-terminal beta-aminopeptidase BapA in complex with hydrolyzed ampicillin
ComponentsBeta-peptidyl aminopeptidase
KeywordsHydrolase/Inhibitor / Ntn-hydrolase / alpha-beta-beta-alpha sandwich / beta-peptide cleaving enzyme / Hydrolase-Inhibitor complex
Function / homology
Function and homology information


beta-peptidyl aminopeptidase / aminopeptidase activity / periplasmic space / proteolysis / identical protein binding
Similarity search - Function
Peptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-OAE / Beta-peptidyl aminopeptidase BapA
Similarity search - Component
Biological speciesSphingosinicella xenopeptidilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMerz, T. / Heck, T. / Geueke, B. / Kohler, H.-P.E. / Gruetter, M.G.
CitationJournal: To be Published
Title: Crystal structure and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family
Authors: Heck, T. / Merz, T. / Geueke, B. / Gruetter, M.G. / Kohler, H.-P.E.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-peptidyl aminopeptidase
B: Beta-peptidyl aminopeptidase
C: Beta-peptidyl aminopeptidase
D: Beta-peptidyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,49618
Polymers154,5394
Non-polymers2,95714
Water22,1401229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18430 Å2
ΔGint-144 kcal/mol
Surface area41950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.300, 97.100, 102.200
Angle α, β, γ (deg.)90.00, 108.70, 90.00
Int Tables number4
Space group name H-MP1211
Detailstetramer of heterodimers

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Components

#1: Protein
Beta-peptidyl aminopeptidase


Mass: 38634.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingosinicella xenopeptidilytica (bacteria)
Gene: bapA / Plasmid: pYBapA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q52VH2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-OAE / (2S,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 367.420 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H21N3O5S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15mg/ml, 1.5M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2009 / Details: dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→49.3 Å / Num. obs: 137090 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.11 / Rsym value: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.98 / Num. unique all: 10556 / Rsym value: 0.455 / % possible all: 99.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N2W

3n2w


Resolution: 1.85→49.3 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1784 1370 1 %RANDOM
Rwork0.1503 ---
obs0.1506 137077 98.45 %-
all-137090 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.383 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1614 Å2-0 Å2-1.1329 Å2
2---5.1948 Å20 Å2
3---5.3563 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10582 0 194 1229 12005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711083
X-RAY DIFFRACTIONf_angle_d1.0515073
X-RAY DIFFRACTIONf_dihedral_angle_d14.7364147
X-RAY DIFFRACTIONf_chiral_restr0.0691732
X-RAY DIFFRACTIONf_plane_restr0.0071988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.21511370.186413619X-RAY DIFFRACTION99
1.9161-1.99280.25961370.171613558X-RAY DIFFRACTION99
1.9928-2.08350.16711360.163413483X-RAY DIFFRACTION98
2.0835-2.19340.22461350.152313340X-RAY DIFFRACTION97
2.1934-2.33080.19491380.155513608X-RAY DIFFRACTION99
2.3308-2.51080.18621370.151413609X-RAY DIFFRACTION99
2.5108-2.76340.18831360.153613507X-RAY DIFFRACTION98
2.7634-3.16320.18191380.147713607X-RAY DIFFRACTION99
3.1632-3.98510.17021370.130213585X-RAY DIFFRACTION98
3.9851-49.30.13271390.143313791X-RAY DIFFRACTION99

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