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- PDB-6v40: Structure of Salmonella Typhi TtsA -

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Basic information

Entry
Database: PDB / ID: 6v40
TitleStructure of Salmonella Typhi TtsA
ComponentsPG_binding_3 domain-containing protein
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
2,6-DIAMINOPIMELIC ACID / Glycoside hydrolase family 108 protein
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.104 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
CitationJournal: 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.
History
DepositionNov 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PG_binding_3 domain-containing protein
B: PG_binding_3 domain-containing protein
C: PG_binding_3 domain-containing protein
D: PG_binding_3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3289
Polymers89,4454
Non-polymers8835
Water5,855325
1
A: PG_binding_3 domain-containing protein
C: PG_binding_3 domain-containing protein
hetero molecules

A: PG_binding_3 domain-containing protein
C: PG_binding_3 domain-containing protein
hetero molecules

B: PG_binding_3 domain-containing protein
D: PG_binding_3 domain-containing protein
hetero molecules

B: PG_binding_3 domain-containing protein
D: PG_binding_3 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,65618
Polymers178,8908
Non-polymers1,76610
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area24750 Å2
ΔGint-69 kcal/mol
Surface area63950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.985, 138.607, 135.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-363-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA7 - 1967 - 196
21ARGARGBB7 - 1967 - 196
12ARGARGAA8 - 1968 - 196
22ARGARGCC8 - 1968 - 196
13ARGARGAA8 - 1968 - 196
23ARGARGDD8 - 1968 - 196
14ARGARGBB8 - 1968 - 196
24ARGARGCC8 - 1968 - 196
15ARGARGBB8 - 1968 - 196
25ARGARGDD8 - 1968 - 196
16LEULEUCC8 - 1978 - 197
26LEULEUDD8 - 1978 - 197

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PG_binding_3 domain-containing protein


Mass: 22361.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY1889 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z6A5
#2: Chemical
ChemComp-API / 2,6-DIAMINOPIMELIC ACID / Diaminopimelic acid


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.59 Å3/Da / Density % sol: 65.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate pH 5.8, 0.1 m NaCl, and 18% v/v (+/-)-2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.1→43.41 Å / Num. obs: 73442 / % possible obs: 98.34 % / Redundancy: 4.9 % / CC1/2: 0.891 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.37
Reflection shellResolution: 2.104→2.179 Å / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 6414 / CC1/2: 0.462

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.104→43.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.828 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.146
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 3698 5 %RANDOM
Rwork0.1912 ---
obs0.1928 69710 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 152.96 Å2 / Biso mean: 51.216 Å2 / Biso min: 27.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.51 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.104→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 60 325 6501
Biso mean--50.6 52.47 -
Num. residues----764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175804
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.6518624
X-RAY DIFFRACTIONr_angle_other_deg1.5311.58713416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.31820.672387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.337151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2491565
X-RAY DIFFRACTIONr_chiral_restr0.10.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027233
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021466
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61760.1
12B61760.1
21A58210.13
22C58210.13
31A59040.13
32D59040.13
41B58850.14
42C58850.14
51B59360.14
52D59360.14
61C60150.11
62D60150.11
LS refinement shellResolution: 2.104→2.159 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 228 -
Rwork0.296 4265 -
all-4493 -
obs--82.12 %
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)
10.6358-0.06230.15510.9214-0.52320.36760.0081-0.15430.2915-0.1297-0.0441-0.02050.14350.00170.03610.11810.0107-0.03480.122-0.02510.179268.17811.9017.995
20.739-0.1876-0.36430.12670.06610.79220.02890.0702-0.05350.0075-0.03220.13270.01410.14270.00330.047900.02190.0607-0.02140.183990.35836.893-10.882
30.804-0.16810.0440.15670.07470.2062-0.0442-0.04410.122-0.05610.0574-0.1083-0.0284-0.001-0.01320.0633-0.0627-0.00450.0820.02510.180247.77134.365-1.666
40.1314-0.3301-0.05630.93070.09470.50530.03250.008-0.0938-0.0384-0.06530.1812-0.0240.00910.03290.0384-0.03090.01210.036-0.02520.259269.78855.4574.483
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 197
2X-RAY DIFFRACTION2B7 - 197
3X-RAY DIFFRACTION3C8 - 197
4X-RAY DIFFRACTION4D8 - 197

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