[English] 日本語
Yorodumi
- PDB-5bmq: Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bmq
TitleCrystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis
ComponentsErfK/YbiS/YcfS/YnhG family protein
KeywordsHYDROLASE / L / D-transpeptidases / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / transferase activity / membrane
Similarity search - Function
: / L,D-transpeptidase (L,D-TPase) catalytic domain profile. / L,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain / PGBD-like superfamily
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / ErfK/YbiS/YcfS/YnhG family protein
Similarity search - Component
Biological speciesStackebrandtia nassauensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsChang, C. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structures of L,D-transpeptidases (Yku)
Authors: Chang, C. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ErfK/YbiS/YcfS/YnhG family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4065
Polymers27,0341
Non-polymers3724
Water4,432246
1
A: ErfK/YbiS/YcfS/YnhG family protein
hetero molecules

A: ErfK/YbiS/YcfS/YnhG family protein
hetero molecules

A: ErfK/YbiS/YcfS/YnhG family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,21815
Polymers81,1013
Non-polymers1,11712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
Buried area4650 Å2
ΔGint-121 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.356, 143.356, 143.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-401-

SO4

21A-401-

SO4

31A-698-

HOH

41A-741-

HOH

-
Components

#1: Protein ErfK/YbiS/YcfS/YnhG family protein


Mass: 27033.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21) (bacteria)
Strain: DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21 / Gene: Snas_6095 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: D3Q1D9, Hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.1 M MES, pH 6.5, 10% dioxane

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 30882 / % possible obs: 99.7 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.077 / Χ2: 0.938 / Net I/av σ(I): 28.674 / Net I/σ(I): 12.7 / Num. measured all: 225239
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.05-2.097.30.8615471.019100
2.09-2.127.30.71515391.006100
2.12-2.167.30.62615171.026100
2.16-2.217.30.54115300.99100
2.21-2.267.40.4515171.019100
2.26-2.317.40.41515630.995100
2.31-2.377.40.32315270.948100
2.37-2.437.40.26615470.943100
2.43-2.57.40.23515330.938100
2.5-2.587.40.18115220.91100
2.58-2.687.40.16315760.899100
2.68-2.787.40.11515280.839100
2.78-2.917.40.0915380.8100
2.91-3.067.40.07115360.811100
3.06-3.257.40.05815450.848100
3.25-3.517.30.05615641.027100
3.51-3.867.30.05215661.141100
3.86-4.427.20.04515701.03999.9
4.42-5.5670.03815580.811100
5.56-506.60.03515590.72294.7

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.05→32.08 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.765 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1781 1521 5 %RANDOM
Rwork0.1536 ---
obs0.1549 28664 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.78 Å2 / Biso mean: 29.718 Å2 / Biso min: 14.22 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.05→32.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 22 246 1875
Biso mean--28.51 44.43 -
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191718
X-RAY DIFFRACTIONr_bond_other_d0.0010.021586
X-RAY DIFFRACTIONr_angle_refined_deg0.9491.9542333
X-RAY DIFFRACTIONr_angle_other_deg0.6573.0023672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9535214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4242576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49715281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.483155
X-RAY DIFFRACTIONr_chiral_restr0.0570.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_rigid_bond_restr1.31133300
X-RAY DIFFRACTIONr_sphericity_free37.503582
X-RAY DIFFRACTIONr_sphericity_bonded8.99953421
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 87 -
Rwork0.172 1713 -
all-1800 -
obs--79.86 %

+
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