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- PDB-3n33: Crystal structure of the N-terminal beta-aminopeptidase BapA in c... -

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Basic information

Entry
Database: PDB / ID: 3n33
TitleCrystal structure of the N-terminal beta-aminopeptidase BapA in complex with pefabloc SC (AEBSF)
ComponentsBeta-peptidyl aminopeptidase
KeywordsHydrolase/Hydrolase Inhibitor / Ntn hydrolase / alpha-beta-beta-alpha sandwich / beta-aminopeptidase / Hydrolase-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
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Beta-peptidyl aminopeptidase BapA
Similarity search - Component
Biological speciesSphingosinicella xenopeptidilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMerz, T. / Heck, T. / Geueke, B. / Kohler, H.-P. / Gruetter, M.G.
CitationJournal: Structure / Year: 2012
Title: Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family.
Authors: Merz, T. / Heck, T. / Geueke, B. / Mittl, P.R. / Briand, C. / Seebach, D. / Kohler, H.P. / Grutter, M.G.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 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)158,54734
Polymers154,5394
Non-polymers4,00830
Water22,7891265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-329 kcal/mol
Surface area41100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.400, 96.850, 101.300
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1295 molecules

#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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1265 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.425 Å / Num. all: 148269 / Num. obs: 144719 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.135 / Rsym value: 0.01 / Net I/σ(I): 12.87
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 3.07 / Num. unique all: 11042 / Rsym value: 0.497 / % possible all: 94.7

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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: 1.8→48.067 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 1448 1 %RANDOM
Rwork0.1596 ---
obs0.1599 144691 97.69 %-
all-144719 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.929 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso mean: 20.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.2989 Å2-0 Å2-2.8579 Å2
2---4.4203 Å20 Å2
3---2.1214 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10628 0 238 1265 12131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711124
X-RAY DIFFRACTIONf_angle_d1.0515122
X-RAY DIFFRACTIONf_dihedral_angle_d13.624030
X-RAY DIFFRACTIONf_chiral_restr0.0671710
X-RAY DIFFRACTIONf_plane_restr0.0081980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86450.26771420.212114023X-RAY DIFFRACTION96
1.8645-1.93920.21761440.200814218X-RAY DIFFRACTION98
1.9392-2.02740.22441420.194314133X-RAY DIFFRACTION97
2.0274-2.13430.2191430.176314102X-RAY DIFFRACTION96
2.1343-2.2680.1961440.156614295X-RAY DIFFRACTION98
2.268-2.44320.21061460.152814429X-RAY DIFFRACTION99
2.4432-2.6890.20221470.152414518X-RAY DIFFRACTION99
2.689-3.07810.18511460.148714448X-RAY DIFFRACTION98
3.0781-3.87780.14751460.131514506X-RAY DIFFRACTION99
3.8778-48.08440.16181480.148914571X-RAY DIFFRACTION98

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