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- PDB-3k3t: E185A mutant of peptidoglycan hydrolase from Sphingomonas sp. A1 -

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Basic information

Entry
Database: PDB / ID: 3k3t
TitleE185A mutant of peptidoglycan hydrolase from Sphingomonas sp. A1
ComponentsPeptidoglycan hydrolase FlgJ
KeywordsHYDROLASE
Function / homology
Function and homology information


amidase activity / hydrolase activity, acting on glycosyl bonds / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / metabolic process / periplasmic space
Similarity search - Function
peptidoglycan hydrolase / Peptidoglycan hydrolase FlgJ / Flagellar protein FlgJ, N-terminal / Rod binding protein / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Complement Module; domain 1 / Lysozyme - #10 / Lysozyme ...peptidoglycan hydrolase / Peptidoglycan hydrolase FlgJ / Flagellar protein FlgJ, N-terminal / Rod binding protein / Lysozyme subfamily 2 / Mannosyl-glycoprotein endo-beta-N-acetylglucosamidase-like domain / Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / Complement Module; domain 1 / Lysozyme - #10 / Lysozyme / Ribbon / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Peptidoglycan hydrolase FlgJ
Similarity search - Component
Biological speciesSphingomonas sp. A1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMaruyama, Y. / Ochiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: J.Basic Microbiol. / Year: 2010
Title: Mutational studies of the peptidoglycan hydrolase FlgJ of Sphingomonas sp. strain A1
Authors: Maruyama, Y. / Ochiai, A. / Itoh, T. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionOct 4, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan hydrolase FlgJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8623
Polymers18,6701
Non-polymers1922
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.441, 54.441, 101.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Peptidoglycan hydrolase FlgJ


Mass: 18669.764 Da / Num. of mol.: 1 / Fragment: residues 152-313 / Mutation: T152M, P153A, E185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. A1 (bacteria) / Gene: flgJ / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7XH69, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM MES pH 6.0, 1.9M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 16152 / Num. obs: 16152 / % possible obs: 99.7 % / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.365 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2zyc

2zyc


Resolution: 1.75→26.29 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.219 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22848 807 5 %RANDOM
Rwork0.19786 ---
obs0.1994 15228 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.157 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 10 123 1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221222
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.9291666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8245162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.17123.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07415186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9041510
X-RAY DIFFRACTIONr_chiral_restr0.0630.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021962
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4561.5769
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88221216
X-RAY DIFFRACTIONr_scbond_it1.3093453
X-RAY DIFFRACTIONr_scangle_it2.2634.5444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 --
Rwork0.249 1091 -
obs--100 %

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