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- PDB-3n2w: Crystal structure of the N-terminal beta-aminopeptidase BapA from... -

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Basic information

Entry
Database: PDB / ID: 3n2w
TitleCrystal structure of the N-terminal beta-aminopeptidase BapA from Sphingosinicella xenopeptidilytica
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: 1.45 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)155,94919
Polymers154,5394
Non-polymers1,40915
Water31,3641741
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-196 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.360, 96.720, 101.420
Angle α, β, γ (deg.)90.00, 108.23, 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)
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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1741 / 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: 53.29 %
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: 1.006 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 1.45→48.809 Å / Num. all: 282888 / Num. obs: 278550 / % possible obs: 98.5 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Rsym value: 0.042 / Net I/σ(I): 16.99
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.67 / Rsym value: 0.433 / % possible all: 92.3

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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 1B65

1b65


Resolution: 1.45→48.809 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / σ(F): 1.99 / Phase error: 13.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1498 6964 2.5 %
Rwork0.1309 --
obs0.1314 278535 98.52 %
all-278550 -
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.577 Å2 / ksol: 0.427 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1676 Å2-0 Å2-1.4753 Å2
2---1.8 Å2-0 Å2
3----0.3676 Å2
Refinement stepCycle: LAST / Resolution: 1.45→48.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10572 0 83 1741 12396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111158
X-RAY DIFFRACTIONf_angle_d1.43815198
X-RAY DIFFRACTIONf_dihedral_angle_d12.5044065
X-RAY DIFFRACTIONf_chiral_restr0.0781751
X-RAY DIFFRACTIONf_plane_restr0.0082009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.26162160.21668410X-RAY DIFFRACTION92
1.4665-1.48370.23362240.20528735X-RAY DIFFRACTION96
1.4837-1.50180.20082290.18658933X-RAY DIFFRACTION97
1.5018-1.52080.20372300.17898964X-RAY DIFFRACTION98
1.5208-1.54090.21052310.17689008X-RAY DIFFRACTION98
1.5409-1.5620.18672330.16449105X-RAY DIFFRACTION99
1.562-1.58430.16982340.15069114X-RAY DIFFRACTION99
1.5843-1.60790.18182330.15139085X-RAY DIFFRACTION99
1.6079-1.63310.16842330.14869106X-RAY DIFFRACTION99
1.6331-1.65980.17242340.14549103X-RAY DIFFRACTION99
1.6598-1.68850.16432340.14499145X-RAY DIFFRACTION99
1.6885-1.71920.16892340.13859128X-RAY DIFFRACTION100
1.7192-1.75220.14932330.13369093X-RAY DIFFRACTION99
1.7522-1.7880.15342330.13179081X-RAY DIFFRACTION99
1.788-1.82690.14922350.12539165X-RAY DIFFRACTION99
1.8269-1.86940.14312330.12679098X-RAY DIFFRACTION99
1.8694-1.91610.1492320.12729040X-RAY DIFFRACTION99
1.9161-1.96790.14542300.12538998X-RAY DIFFRACTION98
1.9679-2.02580.14382320.12099056X-RAY DIFFRACTION98
2.0258-2.09120.15272320.12289029X-RAY DIFFRACTION99
2.0912-2.1660.13882320.12149052X-RAY DIFFRACTION99
2.166-2.25270.15722320.11979054X-RAY DIFFRACTION98
2.2527-2.35520.13652330.11469080X-RAY DIFFRACTION99
2.3552-2.47940.1272310.11129022X-RAY DIFFRACTION98
2.4794-2.63470.12322340.11589128X-RAY DIFFRACTION99
2.6347-2.83810.13972340.12369116X-RAY DIFFRACTION99
2.8381-3.12370.15422340.12869132X-RAY DIFFRACTION99
3.1237-3.57560.14222340.12289098X-RAY DIFFRACTION99
3.5756-4.50430.12232350.11099161X-RAY DIFFRACTION99
4.5043-48.83690.15952400.15619332X-RAY DIFFRACTION99

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