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- PDB-6v3z: Structure of Salmonella enteritidis Sen1395 -

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Basic information

Entry
Database: PDB / ID: 6v3z
TitleStructure of Salmonella enteritidis Sen1395
ComponentsSen1395
KeywordsPROTEIN TRANSPORT / Muramidase Lysozyme-like Peptidoglycan-binding
Function / homology
Function and homology information


TtsA-like, Glycoside hydrolase family 108 domain / Peptidoglycan binding domain / Glycosyl hydrolase 108 / Predicted Peptidoglycan domain / Chitosanase, subunit A; domain 1 / Chitosanase, subunit A, domain 1 / Lysozyme-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 108 protein
Similarity search - Component
Biological speciesSalmonella enteritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGalan, J.E. / Lara-Tejero, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)2R01AI114618-06 United States
Citation
Journal: Elife / Year: 2020
Title: Mechanisms of substrate recognition by a typhoid toxin secretion-associated muramidase.
Authors: Geiger, T. / Lara-Tejero, M. / Xiong, Y. / Galan, J.E.
#1: Journal: To Be Published
Title: Mechanisms of substrate recognition by a typhoid toxin secretion-associated muramidase
Authors: Geiger, T. / Lara-Tejero, M. / Xiong, Y. / Galan, J.E.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sen1395
B: Sen1395


Theoretical massNumber of molelcules
Total (without water)44,9152
Polymers44,9152
Non-polymers00
Water91951
1
A: Sen1395

B: Sen1395


Theoretical massNumber of molelcules
Total (without water)44,9152
Polymers44,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area2790 Å2
ΔGint-24 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.374, 49.371, 58.639
Angle α, β, γ (deg.)91.410, 107.550, 93.610
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 11 - 186 / Label seq-ID: 21 - 196

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Sen1395 / Putative secretion activating protein


Mass: 22457.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enteritidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R2HMX1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7.0 and 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→49.27 Å / Num. obs: 26682 / % possible obs: 89.85 % / Redundancy: 2.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.25
Reflection shellResolution: 1.904→1.972 Å / Rmerge(I) obs: 0.572 / Num. unique obs: 2484 / CC1/2: 0.376

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TTSA

Resolution: 1.9→49.27 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 12.728 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23616 1317 5 %RANDOM
Rwork0.20144 ---
obs0.20315 25201 89.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.678 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å2-3.16 Å21.33 Å2
2--2.73 Å2-1.32 Å2
3----4.16 Å2
Refinement stepCycle: final / Resolution: 1.9→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 0 51 2886
Biso mean---54.34 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172697
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6563899
X-RAY DIFFRACTIONr_angle_other_deg1.4511.5916231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0145354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19220.889180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54315508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9491532
X-RAY DIFFRACTIONr_chiral_restr0.0750.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023293
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02659
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_it3.1064.2121422
X-RAY DIFFRACTIONr_mcbond_other3.1054.2081421
X-RAY DIFFRACTIONr_mcangle_it4.6156.3051774
X-RAY DIFFRACTIONr_mcangle_other4.6146.311775
X-RAY DIFFRACTIONr_scbond_it3.9144.6881471
X-RAY DIFFRACTIONr_scbond_other3.9134.6921472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0586.8322126
X-RAY DIFFRACTIONr_long_range_B_refined9.93678.90912257
X-RAY DIFFRACTIONr_long_range_B_other9.93678.89312242
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5497 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.904→1.954 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 85 -
Rwork0.475 1599 -
all-1684 -
obs--76.72 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0504-0.0527-0.84010.1767-0.22934.04930.02330.42810.11010.1061-0.1365-0.0362-0.13120.28890.11310.1031-0.0450.03110.21480.08580.0885-55.695-44.37739.8875
20.88450.6177-0.72970.6323-0.10791.55350.1262-0.06420.0144-0.03880.02290.0257-0.34060.1607-0.14910.1391-0.005-0.03170.09040.02620.1967-64.4336-53.003532.5644
31.7081-0.4205-0.60280.10390.11936.3211-0.6586-0.1351-0.34830.16210.04060.0846-0.031-0.16350.6180.27920.02850.10460.10420.03330.1169-54.6209-31.526950.4774
40.48640.8167-0.07161.76830.48881.07490.04280.0174-0.00220.084-0.0615-0.0350.089-0.04910.01870.07370.0586-0.03980.09550.03350.2012-42.8011-24.47129.1172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 69
2X-RAY DIFFRACTION2A70 - 186
3X-RAY DIFFRACTION3B10 - 69
4X-RAY DIFFRACTION4B70 - 186

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