[English] 日本語
Yorodumi
- PDB-7cfj: Crystal structure of housekeeping sortase SrtA from Lactobacillus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cfj
TitleCrystal structure of housekeeping sortase SrtA from Lactobacillus rhamnosus GG
ComponentsClass A sortase
KeywordsHYDROLASE / housekeeping sortase / cysteine-transpeptidase / pilus assembly / lactobacillar pilus / SpaCBA pilus / probiotics
Function / homologySortase A / Sortase family / Sortase domain superfamily / Sortase domain / cysteine-type peptidase activity / proteolysis / Class A sortase
Function and homology information
Biological speciesLactobacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPratap, S. / Megta, A.K. / Krishnan, V.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR5891/BRB/10/1098/2012 India
CitationJournal: To Be Published
Title: Crystal structure of housekeeping sortase SrtA from Lactobacillus rhamnosus GG
Authors: Pratap, S. / Megta, A.K. / Krishnan, V.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class A sortase
B: Class A sortase


Theoretical massNumber of molelcules
Total (without water)36,9712
Polymers36,9712
Non-polymers00
Water1267
1
A: Class A sortase


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class A sortase


Theoretical massNumber of molelcules
Total (without water)18,4851
Polymers18,4851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.006, 55.557, 74.897
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 89 - 232 / Label seq-ID: 26 - 169

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Class A sortase / Sortase


Mass: 18485.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus rhamnosus (bacteria)
Gene: F8M46_11135, FEZ43_04140, GKD02_05185, GKD07_00565, GKD11_09430, GKD12_00565, GKD15_01240, GMB04_10630, LRHP344_01784, LRHP540_01088, PY91_04000
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E3D3H8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.97 Å3/Da / Density % sol: 37.47 % / Description: Plate-like
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Citric Bis-Tris Propane, pH 5.0 and 16% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.636→72.712 Å / Num. obs: 3890 / % possible obs: 62.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.071 / Rrim(I) all: 0.116 / Net I/σ(I): 6.1
Reflection shellResolution: 2.636→2.879 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 205 / CC1/2: 0.532 / Rpim(I) all: 0.459 / Rrim(I) all: 0.839 / % possible all: 63.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FN5

3fn5


Resolution: 2.64→72.71 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.849 / SU B: 20.179 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27634 182 4.7 %RANDOM
Rwork0.23895 ---
obs0.24074 3708 45.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.248 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20.02 Å2
2---0.81 Å20 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.64→72.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 0 7 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132064
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171862
X-RAY DIFFRACTIONr_angle_refined_deg1.441.6312821
X-RAY DIFFRACTIONr_angle_other_deg1.2741.5714298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.56826.05671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.051152
X-RAY DIFFRACTIONr_chiral_restr0.0510.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2364.3881150
X-RAY DIFFRACTIONr_mcbond_other3.2364.3891149
X-RAY DIFFRACTIONr_mcangle_it5.2626.5771434
X-RAY DIFFRACTIONr_mcangle_other5.2616.5761435
X-RAY DIFFRACTIONr_scbond_it3.1084.5914
X-RAY DIFFRACTIONr_scbond_other3.1074.501915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0556.6831388
X-RAY DIFFRACTIONr_long_range_B_refined9.3683.0868342
X-RAY DIFFRACTIONr_long_range_B_other9.35983.098342
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4028 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.64→2.705 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.292 13 -
obs--2.1 %

+
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