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

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Basic information

Entry
Database: PDB / ID: 3ndv
TitleCrystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin
ComponentsBeta-peptidyl aminopeptidase
KeywordsHYDROLASE/ANTIBIOTIC / Ntn-hydrolase / beta-aminopeptidase / beta-peptide / alpha-beta-beta-alpha sandwich / N-terminal beta-aminopeptidase / HYDROLASE-ANTIBIOTIC 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-AIC / Chem-NDV / Beta-peptidyl aminopeptidase BapA
Similarity search - Component
Biological speciesSphingosinicella xenopeptidilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMerz, T. / Heck, T. / Geueke, B. / Kohler, H.-P.E. / Gruetter, M.G.
CitationJournal: To be Published
Title: Crystal structures 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 8, 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)157,00814
Polymers154,5394
Non-polymers2,46910
Water20,5011138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-43 kcal/mol
Surface area40950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.900, 96.400, 101.500
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number4
Space group name H-MP1211

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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)
Strain: 3-2W4 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-AIC / (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / AMPICILLIN / D(-)-ALPHA-AMINOBENZYLPENICILLIN / 6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID / Ampicillin


Mass: 349.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H19N3O4S / Comment: antibiotic*YM
#4: Chemical ChemComp-NDV / (2S,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 351.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1138 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15mg/ml protein, 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: Feb 12, 2009 / Details: dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 172088 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Rmerge(I) obs: 0.16 / Rsym value: 0.116 / Net I/σ(I): 9.23
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique all: 70374 / Rsym value: 0.581 / % possible all: 94.4

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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: 1.7→48.835 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
Rfree0.1921 6881 4 %RANDOM
Rwork0.167 ---
obs0.168 172065 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.428 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6686 Å2-0 Å2-0.5142 Å2
2---2.8793 Å20 Å2
3---3.548 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10605 0 168 1138 11911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811035
X-RAY DIFFRACTIONf_angle_d1.10415010
X-RAY DIFFRACTIONf_dihedral_angle_d15.1864090
X-RAY DIFFRACTIONf_chiral_restr0.0711728
X-RAY DIFFRACTIONf_plane_restr0.0091982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72030.27692020.254845X-RAY DIFFRACTION88
1.7203-1.74060.26442190.23315269X-RAY DIFFRACTION95
1.7406-1.76180.27562250.23265384X-RAY DIFFRACTION97
1.7618-1.78410.23342300.22135531X-RAY DIFFRACTION100
1.7841-1.80760.2572300.2035508X-RAY DIFFRACTION100
1.8076-1.83230.22642300.19245518X-RAY DIFFRACTION100
1.8323-1.85850.21342320.18485573X-RAY DIFFRACTION100
1.8585-1.88630.20332310.17355554X-RAY DIFFRACTION100
1.8863-1.91570.20672290.16975505X-RAY DIFFRACTION100
1.9157-1.94720.20332310.16865544X-RAY DIFFRACTION100
1.9472-1.98070.20442290.16835509X-RAY DIFFRACTION100
1.9807-2.01670.21932310.16635539X-RAY DIFFRACTION99
2.0167-2.05550.20032300.16145529X-RAY DIFFRACTION100
2.0555-2.09750.17692300.15665537X-RAY DIFFRACTION99
2.0975-2.14310.18912300.15465502X-RAY DIFFRACTION100
2.1431-2.1930.19942300.15835530X-RAY DIFFRACTION100
2.193-2.24780.18232310.14795540X-RAY DIFFRACTION100
2.2478-2.30860.18842310.1545555X-RAY DIFFRACTION100
2.3086-2.37650.16762300.15545505X-RAY DIFFRACTION100
2.3765-2.45320.18142310.15055559X-RAY DIFFRACTION100
2.4532-2.54090.17992310.15845536X-RAY DIFFRACTION100
2.5409-2.64260.18552320.16165562X-RAY DIFFRACTION100
2.6426-2.76290.17582310.15565548X-RAY DIFFRACTION100
2.7629-2.90850.18792310.15995558X-RAY DIFFRACTION100
2.9085-3.09070.17822320.15625552X-RAY DIFFRACTION100
3.0907-3.32930.17952320.15325559X-RAY DIFFRACTION99
3.3293-3.66420.16622300.14285537X-RAY DIFFRACTION99
3.6642-4.19420.15232330.14215579X-RAY DIFFRACTION99
4.1942-5.28330.15962300.15145538X-RAY DIFFRACTION99
5.2833-48.85470.19812370.19875679X-RAY DIFFRACTION99

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