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- PDB-3vus: Escherichia coli PgaB N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3vus
TitleEscherichia coli PgaB N-terminal domain
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / Poly-beta-1 / 6-N-acetyl-D-glucosamine N-deacetylase / Deacetylase
Function / homology
Function and homology information


macromolecule deacylation / cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / single-species biofilm formation / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process
Similarity search - Function
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / : / 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. ...Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / : / 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 / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.65 Å
AuthorsNishiyama, T. / Noguchi, H. / Yoshida, H. / Park, S.-Y. / Tame, J.R.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The structure of the deacetylase domain of Escherichia coli PgaB, an enzyme required for biofilm formation: a circularly permuted member of the carbohydrate esterase 4 family
Authors: Nishiyama, T. / Noguchi, H. / Yoshida, H. / Park, S.Y. / Tame, J.R.
History
DepositionJul 5, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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_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: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1417
Polymers61,6912
Non-polymers4495
Water3,153175
1
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9703
Polymers30,8461
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1714
Polymers30,8461
Non-polymers3253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.559, 53.114, 144.170
Angle α, β, γ (deg.)90.00, 95.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase / PGA N-deacetylase / Poly-beta-1 / 6-GlcNAc N-deacetylase


Mass: 30845.621 Da / Num. of mol.: 2 / Fragment: deacetylase domain, UNP residues 42-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1023, JW5142, pgaB, ycdR / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: P75906, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACETATE (ACT) B 402 IS NOT FULLY OCCUPIED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.18M Sodium acetate, 0.1M Bis-Tris, 16%(w/v) PEG3350, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A11
SYNCHROTRONPhoton Factory BL-17A21.00938, 0.99957, 0.99321
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 5, 2011
ADSC QUANTUM 315r2CCDJul 5, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.009381
30.999571
40.993211
ReflectionResolution: 1.65→50 Å / Num. all: 69364 / Num. obs: 69364 / % possible obs: 96.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.375 / Num. unique all: 2915 / % possible all: 83.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.6.0119refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.105 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.102 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25633 996 1.4 %RANDOM
Rwork0.20519 ---
obs0.20587 68347 96.6 %-
all-71759 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.448 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 11 175 4445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.024403
X-RAY DIFFRACTIONr_angle_refined_deg2.2941.925976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3795514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31423.305233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24715682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3361536
X-RAY DIFFRACTIONr_chiral_restr0.1710.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213456
LS refinement shellResolution: 1.65→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 68 -
Rwork0.271 4271 -
obs--84.9 %

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