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- PDB-4lgj: Crystal structure and mechanism of a type III secretion protease -

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Basic information

Entry
Database: PDB / ID: 4lgj
TitleCrystal structure and mechanism of a type III secretion protease
ComponentsUncharacterized protein
KeywordsHYDROLASE / Metallopeptidase / a type III secretion protease
Function / homologyNFkB-p65-degrading zinc protease / NFkB-p65-degrading zinc protease / metal ion binding / T3SS secreted effector NleC
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLi, W.Q. / Liu, Y.X. / Sheng, X.L. / Yan, C.Y. / Wang, J.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and mechanism of a type III secretion protease, NleC
Authors: Li, W. / Liu, Y. / Sheng, X. / Yin, P. / Hu, F. / Liu, Y. / Chen, C. / Li, Q. / Yan, C. / Wang, J.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7402
Polymers30,6741
Non-polymers651
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.091, 67.550, 81.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 30674.393 Da / Num. of mol.: 1 / Fragment: UNP residues 23-278 / Mutation: C107S, C132S, C149S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs0847, Z0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X834
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.01 Å3/Da / Density % sol: 38.86 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6
Details: 0.2 M (NH4)2SO4, 100 mM MES pH 6.0, 20% (w/v) polyethylene glycol 3,000, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 69662 / Num. obs: 69523 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.55→1.61 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LGI

4lgi


Resolution: 1.55→39.403 Å / SU ML: 0.15 / σ(F): 1.36 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1835 5.01 %RANDOM
Rwork0.1705 ---
obs0.1717 36637 99.3 %-
all-36895 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.473 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0334 Å2-0 Å20 Å2
2---1.0346 Å20 Å2
3----1.9987 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 1 320 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062099
X-RAY DIFFRACTIONf_angle_d1.1042852
X-RAY DIFFRACTIONf_dihedral_angle_d13.989783
X-RAY DIFFRACTIONf_chiral_restr0.077304
X-RAY DIFFRACTIONf_plane_restr0.004387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58850.26711260.232506X-RAY DIFFRACTION95
1.5885-1.63520.24431350.21372656X-RAY DIFFRACTION100
1.6352-1.6880.20931470.19922677X-RAY DIFFRACTION100
1.688-1.74830.24061220.18452632X-RAY DIFFRACTION100
1.7483-1.81830.21561350.17612709X-RAY DIFFRACTION100
1.8183-1.90110.20371450.17312633X-RAY DIFFRACTION100
1.9011-2.00130.21011410.17922667X-RAY DIFFRACTION100
2.0013-2.12670.19511440.17972701X-RAY DIFFRACTION100
2.1267-2.29090.21351280.16812692X-RAY DIFFRACTION100
2.2909-2.52140.19341600.16522696X-RAY DIFFRACTION100
2.5214-2.88610.19681480.16622670X-RAY DIFFRACTION99
2.8861-3.63580.16921340.16082701X-RAY DIFFRACTION98
3.6358-39.41590.17841700.16082862X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 30.3784 Å / Origin y: 62.7445 Å / Origin z: 10.6187 Å
111213212223313233
T0.0757 Å2-0.0128 Å2-0.0001 Å2-0.1005 Å2-0.0056 Å2--0.0863 Å2
L0.6658 °2-0.3081 °2-0.3537 °2-1.1433 °20.4244 °2--0.805 °2
S0.0303 Å °-0.0462 Å °0.0224 Å °0.0177 Å °0.0048 Å °-0.0549 Å °-0.0266 Å °0.046 Å °0.0048 Å °
Refinement TLS groupSelection details: all

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