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- PDB-3qbu: Crystal structure of putative peptidoglycan deactelyase (HP0310) ... -

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Basic information

Entry
Database: PDB / ID: 3qbu
TitleCrystal structure of putative peptidoglycan deactelyase (HP0310) from Helicobacter pylori
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / metallo enzyme / peptidoglycan / TIM barrel / deacetylase
Function / homology
Function and homology information


acetylxylan esterase / acetylxylan esterase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / xylan catabolic process / cell wall organization / metal ion binding
Similarity search - Function
Peptidoglycan deacetylase PgdA-like / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Peptidoglycan deacetylase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5701 Å
AuthorsShaik, M.M. / Cendron, L. / Percudani, R. / Zanotti, G.
CitationJournal: Plos One / Year: 2011
Title: The Structure of Helicobacter pylori HP0310 Reveals an Atypical Peptidoglycan Deacetylase.
Authors: Shaik, M.M. / Cendron, L. / Percudani, R. / Zanotti, G.
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2013Group: Structure summary
Revision 1.3Sep 13, 2023Group: 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,5298
Polymers150,2674
Non-polymers2624
Water15,547863
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18530 Å2
ΔGint-248 kcal/mol
Surface area37930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.560, 154.730, 158.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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
11ALAALAPROPROchain A and (resseq 2:180 or resseq 182:291 )AA2 - 18035 - 213
12ILEILEARGARGchain A and (resseq 2:180 or resseq 182:291 )AA182 - 291215 - 324
21ALAALAPROPROchain B and (resseq 2:180 or resseq 182:291 )BB2 - 18035 - 213
22ILEILEARGARGchain B and (resseq 2:180 or resseq 182:291 )BB182 - 291215 - 324
31ALAALAPROPROchain C and (resseq 2:180 or resseq 182:291 )CC2 - 18035 - 213
32ILEILEARGARGchain C and (resseq 2:180 or resseq 182:291 )CC182 - 291215 - 324
41ALAALAPROPROchain D and (resseq 2:180 or resseq 182:291 )DD2 - 18035 - 213
42ILEILEARGARGchain D and (resseq 2:180 or resseq 182:291 )DD182 - 291215 - 324

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Components

#1: Protein
Putative uncharacterized protein


Mass: 37566.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: hp0310, HPG27_289 / Plasmid: pET151-hp310 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B5ZA76
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium Sulphate, 0.1M Tri Sodium citrate pH 5.6, 15% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.196
ReflectionResolution: 2.57→69.54 Å / Num. all: 59318 / Num. obs: 59318 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.4
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CL6

3cl6


Resolution: 2.5701→69.54 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3039 5.12 %Random
Rwork0.2042 ---
obs0.2056 59318 97.74 %-
all-59318 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.063 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.3481 Å2-0 Å20 Å2
2---13.7299 Å2-0 Å2
3---26.0779 Å2
Refinement stepCycle: LAST / Resolution: 2.5701→69.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9428 0 4 863 10295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079725
X-RAY DIFFRACTIONf_angle_d1.05513220
X-RAY DIFFRACTIONf_dihedral_angle_d15.9153530
X-RAY DIFFRACTIONf_chiral_restr0.0691375
X-RAY DIFFRACTIONf_plane_restr0.0051692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2349X-RAY DIFFRACTIONPOSITIONAL0.027
12B2349X-RAY DIFFRACTIONPOSITIONAL0.027
13C2349X-RAY DIFFRACTIONPOSITIONAL0.028
14D2349X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5701-2.61450.44931610.38642707X-RAY DIFFRACTION91
2.6145-2.6620.39041650.34182782X-RAY DIFFRACTION92
2.662-2.71320.42251590.33142770X-RAY DIFFRACTION93
2.7132-2.76860.37621490.32212790X-RAY DIFFRACTION93
2.7686-2.82870.33841420.29292833X-RAY DIFFRACTION94
2.8287-2.89450.34591600.28142786X-RAY DIFFRACTION93
2.8945-2.96690.34851510.2762843X-RAY DIFFRACTION94
2.9669-3.04710.25361380.25342821X-RAY DIFFRACTION94
3.0471-3.13670.24811340.24292834X-RAY DIFFRACTION94
3.1367-3.2380.22931440.21862825X-RAY DIFFRACTION94
3.238-3.35360.22931570.20762813X-RAY DIFFRACTION93
3.3536-3.48790.21421560.19652810X-RAY DIFFRACTION93
3.4879-3.64650.1821400.18492848X-RAY DIFFRACTION93
3.6465-3.83870.20021660.16812757X-RAY DIFFRACTION92
3.8387-4.0790.1831610.15822813X-RAY DIFFRACTION92
4.079-4.39370.16241160.15162842X-RAY DIFFRACTION93
4.3937-4.83530.1531520.13182825X-RAY DIFFRACTION93
4.8353-5.53380.1831420.14872852X-RAY DIFFRACTION93
5.5338-6.96750.20741450.18942848X-RAY DIFFRACTION92
6.9675-43.67020.22261680.1722893X-RAY DIFFRACTION90

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