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- PDB-4lpq: Crystal structure of the L,D-transpeptidase (residues 123-326) fr... -

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Basic information

Entry
Database: PDB / ID: 4lpq
TitleCrystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
ComponentsErfK/YbiS/YcfS/YnhG family protein
KeywordsTRANSFERASE / MCSG / LD-transpeptidase / Structural Genomics / Midwest Center for Structural Genomics / L / D-transpeptidase / PSI-Biology
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / cell wall organization / regulation of cell shape / transferase activity / extracellular region
Similarity search - Function
Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / 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 ...Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / PGBD superfamily / L,D-transpeptidase catalytic domain-like / L,D-transpeptidase catalytic domain-like / : / 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 / Peptidoglycan binding-like / Putative peptidoglycan binding domain / PGBD-like superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ErfK/YbiS/YcfS/YnhG family protein
Similarity search - Component
Biological speciesXylanimonas cellulosilytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å
AuthorsNocek, B. / Bigelow, L. / Endres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the L,D-transpeptidase (residues 123-326) from Xylanimonas cellulosilytica DSM 15894
Authors: Nocek, B. / Bigelow, L. / Endres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: ErfK/YbiS/YcfS/YnhG family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1715
Polymers23,0291
Non-polymers1424
Water4,918273
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.849, 62.849, 167.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-750-

HOH

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Components

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


Mass: 23028.896 Da / Num. of mol.: 1 / Mutation: V323T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylanimonas cellulosilytica (bacteria) / Strain: DSM 15894 / CECT 5975 / LMG 20990 / XIL07 / Gene: Xcel_0604 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1BWR1
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.58 Å3/Da / Density % sol: 65.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% Peg6000, 1M Lithium Chloride, 0.1 M Sodium acetate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.37→23.62 Å / Num. all: 71690 / Num. obs: 69682 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 29
Reflection shellResolution: 1.37→1.39 Å / % possible all: 87

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
CCP$model building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.37→23.61 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.195 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS UNIDENTIFY DENSITY AROUND RESIDUE W162. WE WERE UNABLE TO ASSIGN IT THEREFORE IT WAS LEFT UNMODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.14555 3516 5.1 %RANDOM
Rwork0.12187 ---
obs0.1231 66080 97.73 %-
all-69597 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.37→23.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 0 4 273 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191662
X-RAY DIFFRACTIONr_bond_other_d0.0010.021530
X-RAY DIFFRACTIONr_angle_refined_deg2.1761.962277
X-RAY DIFFRACTIONr_angle_other_deg0.96933519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15422.56874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84315232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2631515
X-RAY DIFFRACTIONr_chiral_restr0.1220.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211940
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.61133192
X-RAY DIFFRACTIONr_sphericity_free31.63554
X-RAY DIFFRACTIONr_sphericity_bonded16.16453413
LS refinement shellResolution: 1.371→1.407 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 236 -
Rwork0.24 4574 -
obs--93.18 %

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