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- PDB-6go1: Crystal Structure of a Bacillus anthracis peptidoglycan deacetylase -

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Basic information

Entry
Database: PDB / ID: 6go1
TitleCrystal Structure of a Bacillus anthracis peptidoglycan deacetylase
ComponentsPolysaccharide deacetylase-like protein
KeywordsHYDROLASE / Peptidoglycan / deacetylase / Bacillus anthracis
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3760 / : / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel ...Immunoglobulin-like - #3760 / : / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Polysaccharide deacetylase / Polysaccharide deacetylase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsGiastas, P. / Andreou, A. / Eliopoulos, E.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: The putative polysaccharide deacetylase Ba0331: cloning, expression, crystallization and structure determination.
Authors: Andreou, A. / Giastas, P. / Arnaouteli, S. / Tzanodaskalaki, M. / Tzartos, S.J. / Bethanis, K. / Bouriotis, V. / Eliopoulos, E.E.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Polysaccharide deacetylase-like protein
B: Polysaccharide deacetylase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,40011
Polymers73,8072
Non-polymers5939
Water1,856103
1
A: Polysaccharide deacetylase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2486
Polymers36,9031
Non-polymers3455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polysaccharide deacetylase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1525
Polymers36,9031
Non-polymers2494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.723, 211.795, 46.784
Angle α, β, γ (deg.)90.000, 91.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 50 through 54 or (resid 55...
21(chain B and (resid 50 through 99 or (resid 100...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRILEILE(chain A and (resid 50 through 54 or (resid 55...AA50 - 541 - 5
12THRTHRTHRTHR(chain A and (resid 50 through 54 or (resid 55...AA556
13THRTHRLYSLYS(chain A and (resid 50 through 54 or (resid 55...AA50 - 3671 - 318
14THRTHRLYSLYS(chain A and (resid 50 through 54 or (resid 55...AA50 - 3671 - 318
15THRTHRLYSLYS(chain A and (resid 50 through 54 or (resid 55...AA50 - 3671 - 318
16THRTHRLYSLYS(chain A and (resid 50 through 54 or (resid 55...AA50 - 3671 - 318
17THRTHRLYSLYS(chain A and (resid 50 through 54 or (resid 55...AA50 - 3671 - 318
21THRTHRSERSER(chain B and (resid 50 through 99 or (resid 100...BB50 - 991 - 50
22GLNGLNGLNGLN(chain B and (resid 50 through 99 or (resid 100...BB10051
23THRTHRLYSLYS(chain B and (resid 50 through 99 or (resid 100...BB50 - 3671 - 318
24THRTHRLYSLYS(chain B and (resid 50 through 99 or (resid 100...BB50 - 3671 - 318
25THRTHRLYSLYS(chain B and (resid 50 through 99 or (resid 100...BB50 - 3671 - 318
26THRTHRLYSLYS(chain B and (resid 50 through 99 or (resid 100...BB50 - 3671 - 318

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polysaccharide deacetylase-like protein / Putative polysaccharide deacetylase yxkH


Mass: 36903.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: yxkH, BA_0331, BASH2_05488 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F7RJX5, UniProt: A0A3P1TYX8*PLUS

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Non-polymers , 5 types, 112 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.8 Å3/Da / Density % sol: 56.06 % / Description: Rod shaped
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 150 mM lithium sulfate, 100 mM Tris HCl pH 8.0, 5 mM spermidine, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.589→45.661 Å / Num. obs: 24772 / % possible obs: 98.62 % / Redundancy: 4 % / Biso Wilson estimate: 49.34 Å2 / Net I/σ(I): 1.36
Reflection shellResolution: 2.589→2.693 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V33

4v33


Resolution: 2.59→45.661 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.38
RfactorNum. reflection% reflection
Rfree0.2453 1240 5.01 %
Rwork0.1833 --
obs0.1864 24772 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.65 Å2 / Biso mean: 61.0101 Å2 / Biso min: 23.09 Å2
Refinement stepCycle: final / Resolution: 2.59→45.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5160 0 31 103 5294
Biso mean--75.73 48.4 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015321
X-RAY DIFFRACTIONf_angle_d1.247190
X-RAY DIFFRACTIONf_chiral_restr0.071769
X-RAY DIFFRACTIONf_plane_restr0.008937
X-RAY DIFFRACTIONf_dihedral_angle_d3.8283184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2972X-RAY DIFFRACTION5.838TORSIONAL
12B2972X-RAY DIFFRACTION5.838TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5897-2.69340.32521220.28372325244788
2.6934-2.81590.34071390.274626412780100
2.8159-2.96440.34451410.271126592800100
2.9644-3.150.30781390.232526402779100
3.15-3.39320.28441380.21326362774100
3.3932-3.73450.22841410.179226592800100
3.7345-4.27460.21951400.153526582798100
4.2746-5.38410.20251390.133926442783100
5.3841-45.66790.20751410.157726702811100
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)
11.67011.46430.22971.71740.47012.49810.1833-0.256-0.07-0.6140.0053-0.8214-0.30880.3874-0.2410.90630.16120.08860.4598-0.14060.87831.668-22.503940.8707
22.6048-0.77120.58445.0110.47931.76220.35070.5622-0.7401-0.359-0.4414-0.21670.62730.4733-0.0841.08170.1607-0.05770.5634-0.15141.06627.4669-27.958240.3912
31.45-0.526-1.09281.51740.93621.39650.38160.2457-0.3279-0.8009-0.1652-0.43070.1339-0.0215-0.15130.75140.1687-0.04360.481-0.20450.700324.3924-22.47545.3391
43.17890.27050.13761.8612-0.18382.2398-0.0446-0.3113-0.27580.0010.11390.12270.20830.0671-0.07950.31930.0818-0.00130.3822-0.01590.333511.2508-1.26665.2663
52.57320.3657-0.87253.0030.65570.9080.44640.10310.34720.7353-0.2706-0.1881-0.19160.2287-0.20490.9263-0.1047-0.110.44430.17660.828610.998654.067757.0497
64.7697-2.93372.7742.2026-2.36923.58240.2587-1.1433-0.26120.433-0.2528-0.4837-0.89430.35170.40141.0685-0.2215-0.14860.69390.13461.164815.031761.896863.651
72.57462.1474-0.17314.6071-0.7121.64540.35780.34250.72160.6979-0.1820.0998-0.51020.1454-0.03190.8148-0.1273-0.04050.42120.15550.75729.473758.17255.8542
83.77753.45661.56828.48372.00842.81210.56880.11990.25681.4328-0.2643-0.5757-0.3355-0.0855-0.04470.8596-0.06460.02510.3788-0.01110.6173.267443.513554.2809
97.56033.65481.5828.31831.34196.70590.0920.3665-0.1986-0.4942-0.0397-0.27180.0065-0.5973-0.32880.31580.04250.00630.47540.02480.2959-18.723922.506744.5885
107.4291-4.1233-2.08828.65612.02667.9375-0.19270.5286-0.53830.4823-0.1908-0.18450.6159-0.80350.55030.23220.01680.0260.4609-0.03360.4034-21.99417.238846.0092
115.27211.719-0.25195.54831.17866.7519-0.33160.60651.1741-0.21970.170.5952-0.7996-0.73550.09250.55520.15360.01470.49490.24780.5587-19.830336.149142.7947
122.9587-0.30570.33434.11220.90493.88850.09750.52680.6025-0.2869-0.1763-0.0557-0.5626-0.0061-0.00510.33180.00960.00840.43630.13630.3101-8.223831.446740.6232
132.4470.29330.86053.3158-1.16893.81730.14880.5569-0.1543-0.25480.15350.0551-0.0130.3103-0.27140.29810.0217-0.00820.4898-0.0590.2507-3.916615.963239.8194
143.45911.26682.95356.63952.98636.971-0.40431.39660.3316-0.70060.1159-0.42810.17690.57850.12390.36880.0330.12160.6795-0.030.3783.631119.431936.0878
155.7389-1.5895-0.49873.9356-0.53934.9032-0.09090.05240.30150.3431-0.0582-0.40460.2898-0.11060.01390.2672-0.0247-0.06620.3280.01770.29993.348918.478351.8915
164.97881.59572.6276.78022.20823.09780.4159-0.4402-0.44060.698-0.23220.2796-0.15680.4276-0.16860.5075-0.0214-0.02260.40270.01050.3559-1.38329.089358.5063
178.606-0.6692.98983.1394-0.67142.56220.1471-0.4068-0.21660.341-0.01020.4147-0.4753-0.4902-0.110.37450.0606-0.00260.36330.02250.2962-12.862430.318453.8104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 86 )A50 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 106 )A87 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 154 )A107 - 154
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 367 )A155 - 367
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 96 )B50 - 96
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 106 )B97 - 106
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 139 )B107 - 139
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 150 )B140 - 150
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 162 )B151 - 162
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 173 )B163 - 173
11X-RAY DIFFRACTION11chain 'B' and (resid 174 through 187 )B174 - 187
12X-RAY DIFFRACTION12chain 'B' and (resid 188 through 245 )B188 - 245
13X-RAY DIFFRACTION13chain 'B' and (resid 246 through 290 )B246 - 290
14X-RAY DIFFRACTION14chain 'B' and (resid 291 through 304 )B291 - 304
15X-RAY DIFFRACTION15chain 'B' and (resid 305 through 329 )B305 - 329
16X-RAY DIFFRACTION16chain 'B' and (resid 330 through 343 )B330 - 343
17X-RAY DIFFRACTION17chain 'B' and (resid 344 through 367 )B344 - 367

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