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- PDB-4ztk: Transpeptidase domain of FtsI4 D,D-transpeptidase from Legionella... -

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Basic information

Entry
Database: PDB / ID: 4ztk
TitleTranspeptidase domain of FtsI4 D,D-transpeptidase from Legionella pneumophila.
ComponentsCell division protein FtsI/penicillin binding protein 2
KeywordsTransferase / Cell Cycle / D / D-transpeptidase / FtsI / structural genomics / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homologyBeta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 Å
AuthorsCUFF, M. / OSIPIUK, J. / WU, R. / ENDRES, M. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: to be published
Title: Transpeptidase domain of FtsI4 D,D-transpeptidase from Legionella pneumophila.
Authors: CUFF, M. / OSIPIUK, J. / WU, R. / ENDRES, M. / JOACHIMIAK, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein FtsI/penicillin binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2332
Polymers34,0251
Non-polymers2071
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.376, 72.057, 75.456
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division protein FtsI/penicillin binding protein 2 /


Mass: 34025.434 Da / Num. of mol.: 1 / Mutation: UNP residues 324-636
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_1557 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8UTM2
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.91 Å3/Da / Density % sol: 35.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES-NaOH buffer, 30% PEG 400

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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: Feb 9, 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: 2.1→50 Å / Num. all: 15303 / Num. obs: 15303 / % possible obs: 98.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 40.14 Å2 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.048 / Rrim(I) all: 0.118 / Χ2: 1.727 / Net I/av σ(I): 21.442 / Net I/σ(I): 9 / Num. measured all: 87973
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.145.50.7827620.7110.3560.860.88599.2
2.14-2.185.70.6417390.7920.2910.7060.93698.9
2.18-2.225.80.5587720.840.2550.6160.938100
2.22-2.265.80.4827580.8540.2170.531.01298.4
2.26-2.315.90.4637550.8870.2090.5091.043100
2.31-2.375.80.3957500.90.180.4351.05898.7
2.37-2.425.90.3297550.9350.1480.3621.173100
2.42-2.495.80.2837610.9470.1280.3121.20298.3
2.49-2.565.90.257600.9630.1120.2751.276100
2.56-2.655.90.2077510.9760.0930.2281.39198.2
2.65-2.745.80.1697760.9860.0760.1851.471100
2.74-2.855.90.1557390.9820.0690.171.55598.1
2.85-2.985.80.1397780.9830.0620.1521.76498.2
2.98-3.145.80.1157660.9880.0510.1261.92998.6
3.14-3.335.80.1067650.9930.0470.1162.2799.1
3.33-3.595.80.0987830.9880.0440.1072.44297.9
3.59-3.955.80.0947550.9920.0420.1042.39997.2
3.95-4.525.60.0787770.9940.0350.0862.48998.1
4.52-5.75.50.0747770.9950.0330.0813.21496.5
5.7-505.10.0818240.9930.0390.094.24993.4

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.104→39.586 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2192 765 5.01 %
Rwork0.167 14500 -
obs0.1695 15265 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.91 Å2 / Biso mean: 45.6355 Å2 / Biso min: 18.81 Å2
Refinement stepCycle: final / Resolution: 2.104→39.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 13 60 2087
Biso mean--51.54 45.74 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042060
X-RAY DIFFRACTIONf_angle_d0.8442793
X-RAY DIFFRACTIONf_chiral_restr0.059329
X-RAY DIFFRACTIONf_plane_restr0.003357
X-RAY DIFFRACTIONf_dihedral_angle_d12.404749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1042-2.26660.26771530.20532826297997
2.2666-2.49470.27191520.19142880303299
2.4947-2.85560.23631550.17722881303699
2.8556-3.59740.23971520.18032942309499
3.5974-39.59330.1871530.14872971312496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.68670.5872-0.36511.52490.17921.1519-0.1443-0.42520.00580.23210.06810.128-0.0049-0.16410.00010.33880.03250.03230.38210.01280.25513.502934.269829.1815
20.4826-0.1164-0.11320.1233-0.10020.23320.02020.0553-0.4683-0.1072-0.18230.69750.3497-0.9260.0020.2607-0.07620.0540.4742-0.02820.45564.748427.855820.7283
31.7523-0.82020.01623.07670.30622.87170.0770.1469-0.0949-0.21060.0733-0.19230.25830.21240.00190.23820.0124-0.01580.2256-0.01460.245224.449930.3659.1487
41.4153-0.0218-1.71023.7150.01412.85310.0454-0.00670.17160.05490.04280.1492-0.2552-0.33150.00280.23550.01780.0080.2302-0.02140.227313.916641.047418.3538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 383 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 384 through 398 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 399 through 565 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 566 through 632 )A0

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