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- PDB-4lzh: L,D-transpeptidase from Klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 4lzh
TitleL,D-transpeptidase from Klebsiella pneumoniae
ComponentsL,D-transpeptidase
KeywordsTRANSFERASE / structural genomics / APC110661 / L / D-transpeptidase / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / glycosyltransferase activity / cell wall organization / regulation of cell shape / periplasmic space / extracellular region
Similarity search - Function
L,D-transpeptidase C-terminal domain / L,D-transpeptidase C-terminal domain / : / 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
Similarity search - Domain/homology
L,D-TPase catalytic domain-containing protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: L,D-transpeptidase from Klebsiella pneumoniae.
Authors: Osipiuk, J. / Hatzos-Skintges, C. / Endres, M. / Joachimiak, A.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 30, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L,D-transpeptidase


Theoretical massNumber of molelcules
Total (without water)31,3261
Polymers31,3261
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.746, 150.746, 43.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein L,D-transpeptidase


Mass: 31325.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 / Gene: KPN78578_08240, KPN_00849, ybiS / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6T6R4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M k/Na tartrate, 0.1 M Tris buffer, 0.2 M lithium sulfate, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→37.7 Å / Num. all: 28687 / Num. obs: 28687 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.599 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.933.90.9362.514400.9100
1.93-1.9740.7214350.936100
1.97-2.014.10.65114690.94100
2.01-2.054.10.53114211.058100
2.05-2.094.10.45214291.039100
2.09-2.144.10.40214381.1100
2.14-2.194.10.34414161.206100
2.19-2.254.10.31214611.29100
2.25-2.324.10.26814191.431100
2.32-2.394.10.2414271.469100
2.39-2.484.20.22514431.514100
2.48-2.584.10.19214201.633100
2.58-2.74.10.1714511.786100
2.7-2.844.10.14914241.846100
2.84-3.024.10.12314361.9799.9
3.02-3.254.10.10214411.92399.9
3.25-3.584.10.0914291.959100
3.58-4.094.10.08114221.92899.7
4.09-5.1640.06614402.34699.7
5.16-504.10.07514263.68599.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 4.709 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 1456 5.1 %RANDOM
Rwork0.1508 ---
all0.1523 28687 --
obs0.1523 28687 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.34 Å2 / Biso mean: 26.383 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.32 Å20 Å2
2--0.32 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2135 0 0 183 2318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0192311
X-RAY DIFFRACTIONr_bond_other_d0.0040.022241
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9773183
X-RAY DIFFRACTIONr_angle_other_deg0.84735178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03924.906106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.11915361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5951514
X-RAY DIFFRACTIONr_chiral_restr0.1080.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 110 -
Rwork0.206 2024 -
all-2134 -
obs-2134 98.8 %
Refinement TLS params.Method: refined / Origin x: 35.2636 Å / Origin y: 20.2237 Å / Origin z: 10.741 Å
111213212223313233
T0.0233 Å20.0163 Å2-0.007 Å2-0.0281 Å2-0 Å2--0.0069 Å2
L0.1869 °2-0.3526 °20.0842 °2-0.7783 °2-0.0811 °2--0.1749 °2
S-0.0312 Å °-0.0226 Å °0.0146 Å °0.0541 Å °0.0298 Å °-0.0113 Å °-0.009 Å °-0.0493 Å °0.0014 Å °

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