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- PDB-3n5i: Crystal structure of the precursor (S250A mutant) of the N-termin... -

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Basic information

Entry
Database: PDB / ID: 3n5i
TitleCrystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA
ComponentsBeta-peptidyl aminopeptidase
KeywordsHYDROLASE / Ntn hydrolase / alpha-beta-beta-alpha sandwich / beta-aminopeptidase / beta-peptide
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
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 25, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)155,32413
Polymers154,4754
Non-polymers8499
Water20,2491124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17270 Å2
ΔGint-114 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.700, 113.700, 126.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Beta-peptidyl aminopeptidase


Mass: 38618.836 Da / Num. of mol.: 4 / Mutation: S250A
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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.0 - 1.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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 22, 2008 / Details: dynamically bendable mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.399 Å / Num. obs: 131688 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.071 / Net I/σ(I): 15.64
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.96 / Num. unique all: 19497 / Rsym value: 0.473 / % possible all: 99.2

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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: single chain of PDB code 3N2W, w/o aa 231-250

3n2w


Resolution: 1.8→29.394 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1801 2634 2 %random
Rwork0.1543 ---
obs0.1549 131659 99.15 %-
all-131688 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.421 Å2 / ksol: 0.373 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9488 Å20 Å2-0 Å2
2--5.3411 Å2-0 Å2
3----6.2899 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10557 0 49 1124 11730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910876
X-RAY DIFFRACTIONf_angle_d1.13814781
X-RAY DIFFRACTIONf_dihedral_angle_d12.3383903
X-RAY DIFFRACTIONf_chiral_restr0.0691705
X-RAY DIFFRACTIONf_plane_restr0.0051953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83270.23341360.19376692X-RAY DIFFRACTION99
1.8327-1.8680.23881390.19486772X-RAY DIFFRACTION99
1.868-1.90610.30061360.216679X-RAY DIFFRACTION99
1.9061-1.94750.21121370.18246700X-RAY DIFFRACTION99
1.9475-1.99280.18951380.15886785X-RAY DIFFRACTION100
1.9928-2.04270.19091380.15156731X-RAY DIFFRACTION99
2.0427-2.09790.17411370.15256723X-RAY DIFFRACTION99
2.0979-2.15960.18591380.14436783X-RAY DIFFRACTION100
2.1596-2.22930.17841390.15626771X-RAY DIFFRACTION99
2.2293-2.30890.1971360.15946684X-RAY DIFFRACTION99
2.3089-2.40130.20551390.15366816X-RAY DIFFRACTION99
2.4013-2.51050.22621390.15786784X-RAY DIFFRACTION99
2.5105-2.64280.17871380.15256792X-RAY DIFFRACTION99
2.6428-2.80830.16371390.15636775X-RAY DIFFRACTION99
2.8083-3.02490.17071390.15056847X-RAY DIFFRACTION99
3.0249-3.32890.15241400.14316825X-RAY DIFFRACTION99
3.3289-3.80980.13481390.1326850X-RAY DIFFRACTION99
3.8098-4.79650.13451410.13016878X-RAY DIFFRACTION99
4.7965-29.39820.19251460.16297138X-RAY DIFFRACTION99

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