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- PDB-4r29: Crystal structure of bacterial cysteine methyltransferase effecto... -

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Basic information

Entry
Database: PDB / ID: 4r29
TitleCrystal structure of bacterial cysteine methyltransferase effector NleE
ComponentsUncharacterized protein
KeywordsTRANSFERASE / Rossmann-like Fold / NF-kappaB inhibition / TAB2 and TAB3
Function / homologyCITRIC ACID / S-ADENOSYLMETHIONINE / T3SS effector protein NleE
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsYao, Q. / Chen, J. / Hu, L. / Zhang, L. / Shao, F.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway.
Authors: Yao, Q. / Zhang, L. / Wan, X. / Chen, J. / Hu, L. / Ding, X. / Li, L. / Karar, J. / Peng, H. / Chen, S. / Huang, N. / Rauscher, F.J. / Shao, F.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,37313
Polymers104,1194
Non-polymers2,2549
Water5,314295
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5203
Polymers26,0301
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6203
Polymers26,0301
Non-polymers5912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7124
Polymers26,0301
Non-polymers6833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5203
Polymers26,0301
Non-polymers4912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.304, 53.976, 134.794
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein / Cysteine methyltransferase / NleE


Mass: 26029.771 Da / Num. of mol.: 4 / Mutation: E181A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ECs3858, Z4329 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DBA6
#2: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.34 Å3/Da / Density % sol: 47.46 %

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→20.02 Å / Num. all: 43485 / Num. obs: 42616 / % possible obs: 99.8 % / Observed criterion σ(F): 261.7 / Observed criterion σ(I): 57.3 / Redundancy: 3.7 %
Reflection shellResolution: 2.3→2.34 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→20.02 Å / SU ML: 0.26 / σ(F): 0.04 / Phase error: 23.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1943 4.72 %RANDOM
Rwork0.1974 ---
obs0.1991 41197 96.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.751 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.986 Å20 Å2-0.4349 Å2
2--3.9501 Å20 Å2
3----2.9641 Å2
Refinement stepCycle: LAST / Resolution: 2.31→20.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 152 295 7034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086895
X-RAY DIFFRACTIONf_angle_d1.1089310
X-RAY DIFFRACTIONf_dihedral_angle_d18.3292677
X-RAY DIFFRACTIONf_chiral_restr0.075975
X-RAY DIFFRACTIONf_plane_restr0.0051195
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3103-2.39270.2921750.2247350686
2.3927-2.48830.28051880.2154377994
2.4883-2.60140.2721900.2149387395
2.6014-2.73820.27031900.2129386096
2.7382-2.90930.25371930.2062392597
2.9093-3.13310.25252010.2138401598
3.1331-3.4470.24171960.1965399699
3.447-3.94240.2061980.1816402899
3.9424-4.95460.18532050.1658410199
4.9546-20.02090.23552070.2111417199

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