[English] 日本語
Yorodumi
- PDB-1ysj: Crystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ysj
TitleCrystal Structure of Bacillus Subtilis YXEP Protein (APC1829), a Dinuclear Metal Binding Peptidase from M20 Family
Componentsprotein yxeP
KeywordsHYDROLASE / M20 family Peptidase / Dinuclear Metal Binding / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


cysteine biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity / metal ion binding
Similarity search - Function
Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidohydrolase / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / N-acetylcysteine deacetylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of Bacillus Subtilis YXEP Protein, a Dinuclear Metal Binding Peptidase from M20 Family
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Collart, F.R. / Anderson, W.F.
History
DepositionFeb 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: protein yxeP
B: protein yxeP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9196
Polymers89,6842
Non-polymers2354
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-59 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.854, 42.157, 75.449
Angle α, β, γ (deg.)90.00, 106.713, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer generated from chains A and B

-
Components

#1: Protein protein yxeP


Mass: 44841.969 Da / Num. of mol.: 2 / Mutation: A54G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yxeP / Plasmid: PMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P54955, N-acyl-aliphatic-L-amino acid amidohydrolase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25M NaCl, 0.1M MES, 25% PEG 1000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.97857 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2004 / Details: MIRROR
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 28357 / Num. obs: 28357 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2508 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERV. 1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1xmb

1xmb


Resolution: 2.4→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.064 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.687 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24709 1427 5.1 %RANDOM
Rwork0.18173 ---
obs0.18501 26357 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.265 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.6 Å2
2--0.85 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 4 312 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225765
X-RAY DIFFRACTIONr_angle_refined_deg0.9141.9427827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84524.532278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40515963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8441538
X-RAY DIFFRACTIONr_chiral_restr0.0630.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024452
X-RAY DIFFRACTIONr_nbd_refined0.1720.22875
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2365
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.28
X-RAY DIFFRACTIONr_mcbond_it1.2931.53727
X-RAY DIFFRACTIONr_mcangle_it1.72125813
X-RAY DIFFRACTIONr_scbond_it3.07632291
X-RAY DIFFRACTIONr_scangle_it4.6914.52014
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 106 -
Rwork0.22 1746 -
obs--89.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5323-0.17560.20361.792-0.73133.4984-0.0051-0.37030.080.15740.0743-0.1058-0.29230.0742-0.0692-0.185-0.0090.0165-0.2007-0.0047-0.137234.30117.815848.725
27.721-0.61614.59910.9492-1.06743.28460.36980.1726-0.6131-0.1675-0.05680.12950.2041-0.1933-0.313-0.06570.04860.00870.14890.01430.06393.1546-2.079935.6546
33.0135-1.15251.11273.0323-0.68621.68610.0423-0.0081-0.2676-0.32070.0242-0.01350.1458-0.0323-0.0664-0.0845-0.02250.0175-0.175-0.0162-0.1424-22.49342.9061-8.8501
44.1698-0.12336.15970.9266-0.85159.5848-0.29990.18160.30010.2264-0.0429-0.1244-0.69040.29160.34280.13180.0128-0.00960.1959-0.0314-0.0541-10.331413.342121.958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 17126 - 195
2X-RAY DIFFRACTION1AA298 - 379322 - 403
3X-RAY DIFFRACTION2AA172 - 297196 - 321
4X-RAY DIFFRACTION3BB3 - 17127 - 195
5X-RAY DIFFRACTION3BB298 - 379322 - 403
6X-RAY DIFFRACTION4BB172 - 297196 - 321

+
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://pdbjlvh1.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