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- PDB-6ai4: Structure of Transferase mutant-C21S,C199S -

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Basic information

Entry
Database: PDB / ID: 6ai4
TitleStructure of Transferase mutant-C21S,C199S
ComponentsNon-LEE encoded effector protein NleB
KeywordsTRANSFERASE
Function / homologySseK/NleB family / transferase activity / T3SS effector NleB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPark, J.B. / Yoo, Y. / Kim, J.
CitationJournal: To Be Published
Title: Transferase mutant-C21S,C199S
Authors: Park, J.B. / Yoo, Y. / Kim, J.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-LEE encoded effector protein NleB
B: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)76,1482
Polymers76,1482
Non-polymers00
Water2,468137
1
A: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)38,0741
Polymers38,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-LEE encoded effector protein NleB


Theoretical massNumber of molelcules
Total (without water)38,0741
Polymers38,0741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.820, 95.520, 120.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Non-LEE encoded effector protein NleB


Mass: 38073.988 Da / Num. of mol.: 2 / Mutation: C21S, C199S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nleB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D7C3R7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion / Details: 0.8M LiCl2, 0.1M Tris-HCl (pH8.5), 8%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→67.8 Å / Num. obs: 45767 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.941 / Num. unique obs: 2651

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H60

5h60


Resolution: 2.1→44.42 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.621 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29806 2311 5 %RANDOM
Rwork0.26053 ---
obs0.26239 43743 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.772 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.1→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 0 137 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0144770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174220
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.6496426
X-RAY DIFFRACTIONr_angle_other_deg1.0071.6389896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54322.569288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21815854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4361531
X-RAY DIFFRACTIONr_chiral_restr0.0590.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02935
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_it3.4644.7322250
X-RAY DIFFRACTIONr_mcbond_other3.4644.7312249
X-RAY DIFFRACTIONr_mcangle_it5.0367.0812802
X-RAY DIFFRACTIONr_mcangle_other5.0357.0812803
X-RAY DIFFRACTIONr_scbond_it3.8435.1032520
X-RAY DIFFRACTIONr_scbond_other3.8425.1042521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6777.4973625
X-RAY DIFFRACTIONr_long_range_B_refined8.27688.26519861
X-RAY DIFFRACTIONr_long_range_B_other8.27488.28319822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 144 -
Rwork0.328 3235 -
obs--99.76 %

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