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- PDB-6hc7: The crystal structure of BSAP, a zinc aminopeptidase from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 6hc7
TitleThe crystal structure of BSAP, a zinc aminopeptidase from Bacillus subtilis (medium resolution)
ComponentsAminopeptidase Y (Arg Lys Leu preference)
KeywordsMETAL BINDING PROTEIN / aminopeptidase / bacillus subtilis / PA-domain / zinc enzyme
Function / homology
Function and homology information


aminopeptidase B / bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28 family / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
ACETATE ION / Aminopeptidase Y (Arg Lys Leu preference) / Aminopeptidase YwaD
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlhadeff, R. / Lansky, S. / Feinberg, H. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: The crystal structure of BSAP, a zinc aminopeptidase from Bacillus subtilis (medium resolution)
Authors: Alhadeff, R. / Faygenboim, R. / Lansky, S. / Rogoulenko, E. / Cohen, T. / Fundoiano-Hershcovitz, Y. / Feinberg, H. / Shoham, Y. / Shoham, G.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase Y (Arg Lys Leu preference)
B: Aminopeptidase Y (Arg Lys Leu preference)
C: Aminopeptidase Y (Arg Lys Leu preference)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,61621
Polymers148,5453
Non-polymers1,07018
Water6,233346
1
A: Aminopeptidase Y (Arg Lys Leu preference)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9337
Polymers49,5151
Non-polymers4176
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase Y (Arg Lys Leu preference)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8727
Polymers49,5151
Non-polymers3576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminopeptidase Y (Arg Lys Leu preference)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8117
Polymers49,5151
Non-polymers2966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-329 kcal/mol
Surface area49880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.833, 225.833, 42.654
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Aminopeptidase Y (Arg Lys Leu preference)


Mass: 49515.082 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_2172 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164UP62, UniProt: P25152*PLUS

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Non-polymers , 5 types, 364 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 2K MME, 0.1M LiSO4, 4mM MnCl2, 0.1M acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.282 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.5→74 Å / Num. obs: 43610 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.25 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CP7

1cp7


Resolution: 2.5→73.921 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.15
RfactorNum. reflection% reflection
Rfree0.2514 2170 4.98 %
Rwork0.1777 --
obs0.1814 43610 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→73.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9323 0 39 346 9708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099515
X-RAY DIFFRACTIONf_angle_d1.17212863
X-RAY DIFFRACTIONf_dihedral_angle_d15.5413521
X-RAY DIFFRACTIONf_chiral_restr0.0441439
X-RAY DIFFRACTIONf_plane_restr0.0061672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55820.30091250.21942513X-RAY DIFFRACTION92
2.5582-2.62220.32131340.21392728X-RAY DIFFRACTION98
2.6222-2.69310.27751420.20482729X-RAY DIFFRACTION100
2.6931-2.77230.33281460.22582741X-RAY DIFFRACTION100
2.7723-2.86180.34871460.22872766X-RAY DIFFRACTION100
2.8618-2.96410.30011430.21462723X-RAY DIFFRACTION100
2.9641-3.08280.28561350.21182778X-RAY DIFFRACTION100
3.0828-3.22310.29311610.2072756X-RAY DIFFRACTION100
3.2231-3.3930.26451340.19532769X-RAY DIFFRACTION100
3.393-3.60560.24481420.17572796X-RAY DIFFRACTION100
3.6056-3.88390.25491540.16842791X-RAY DIFFRACTION100
3.8839-4.27470.21641280.15222805X-RAY DIFFRACTION100
4.2747-4.89320.20671610.13662778X-RAY DIFFRACTION100
4.8932-6.16450.22951690.16392831X-RAY DIFFRACTION100
6.1645-73.95350.20241500.15522936X-RAY DIFFRACTION100

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