[English] 日本語
Yorodumi
- PDB-6hc7: The crystal structure of BSAP, a zinc aminopeptidase from Bacillu... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Sulfate


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


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


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


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more