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- PDB-3i18: Crystal Structure of the PDZ domain of the SdrC-like protein (Lmo... -

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Basic information

Entry
Database: PDB / ID: 3i18
TitleCrystal Structure of the PDZ domain of the SdrC-like protein (Lmo2051) from Listeria monocytogenes, Northeast Structural Genomics Consortium Target LmR166B
ComponentsLmo2051 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding / membrane
Similarity search - Function
PDZ domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / PDZ domain / PDZ superfamily ...PDZ domain / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / PDZ domain / PDZ superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Roll / Ribosomal protein S5 domain 2-type fold / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / endopeptidase La
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target LmR166B
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: Lmo2051 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2842
Polymers11,2041
Non-polymers801
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.705, 90.475, 51.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lmo2051 protein


Mass: 11204.261 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2051 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8Y5K8
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLEU134 WAS MUTATED TO MET SO THAT THE STRUCTURE COULD BE DETERMINED USING SE ANOMALOUS SIGNAL.

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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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 291 K / Method: microbatch, under oil / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 30% w/v Polyethylene glycol monomethyl ether 2k and 150mM Potassium Bromide, microbatch, under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 17896 / Num. obs: 14872 / % possible obs: 83.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.054 / Net I/σ(I): 32.6
Reflection shellResolution: 1.7→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 9.4 / Num. unique all: 1784 / Rsym value: 0.106 / % possible all: 61.2

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→17.85 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 586592.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 735 5 %RANDOM
Rwork0.193 ---
all0.195 17855 --
obs0.194 14838 83.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.418 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---1.65 Å20 Å2
3---2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→17.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 1 122 858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.243 71 6.5 %
Rwork0.171 1022 -
obs-1093 61.5 %

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