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- PDB-1r77: Crystal structure of the cell wall targeting domain of peptidylgl... -

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Basic information

Entry
Database: PDB / ID: 1r77
TitleCrystal structure of the cell wall targeting domain of peptidylglycan hydrolase ALE-1
ComponentsCell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1
KeywordsHYDROLASE / SH3b Domain / Cell Wall Targeting Domain / Lysostaphin / Peptidoglycan Hydrolase / Glycylglycine Endopeptidase
Function / homology
Function and homology information


lysostaphin / cell wall organization / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / SH3 Domains / SH3 type barrels. ...Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / SH3 Domains / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Glycyl-glycine endopeptidase ALE-1
Similarity search - Component
Biological speciesStaphylococcus capitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLu, J.Z. / Fujiwara, T. / Komatsuzawa, H. / Sugai, M. / Sakon, J.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Cell Wall-targeting Domain of Glycylglycine Endopeptidase Distinguishes among Peptidoglycan Cross-bridges.
Authors: Lu, J.Z. / Fujiwara, T. / Komatsuzawa, H. / Sugai, M. / Sakon, J.
#1: Journal: J.Bacteriol. / Year: 1997
Title: Purification and molecular characterization of glycylglycine endopeptidase produced by Staphylococcus capitis EPK1.
Authors: Sugai, M. / Fujiwara, T. / Akiyama, T. / Ohara, M. / Komatsuzawa, H. / Inoue, S. / Suginaka, H.
History
DepositionOct 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE FLAG-tag was added to the N-terminus

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1
B: Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1


Theoretical massNumber of molelcules
Total (without water)23,5192
Polymers23,5192
Non-polymers00
Water3,981221
1
A: Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1


Theoretical massNumber of molelcules
Total (without water)11,7591
Polymers11,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1


Theoretical massNumber of molelcules
Total (without water)11,7591
Polymers11,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.199, 58.521, 85.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell Wall Targeting Domain of Glycylglycine Endopeptidase ALE-1


Mass: 11759.253 Da / Num. of mol.: 2 / Fragment: Cell Wall Targeting Domain / Mutation: FLAG-tag added at N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus capitis (bacteria) / Strain: EPK1 / Plasmid: pTF479 / Production host: Escherichia coli (E. coli) / References: UniProt: O05156, interstitial collagenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, sodium acetate, MES pH 6.5 or HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONAPS 17-ID10.97931, 0.97917, 0.95370
SYNCHROTRONAPS 17-ID21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 30, 2001
MARRESEARCH2CCDAug 18, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)MADMx-ray1
2Si (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979171
30.95371
411
ReflectionResolution: 1.75→20 Å / Num. all: 23430 / Num. obs: 22012 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 13.5 Å2
Reflection shellResolution: 1.75→1.81 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminus truncated SeMet MAD structure

Resolution: 1.75→17.5 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 250222.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1073 4.9 %RANDOM
Rwork0.202 ---
all0.202 23430 --
obs0.202 22012 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2203 Å2 / ksol: 0.389424 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--4.28 Å20 Å2
3----3.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.75→17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 0 221 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.772
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 153 4.9 %
Rwork0.254 2974 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMCBS_TOPPAR:WATER.TOP

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