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- PDB-5jmu: The crystal structure of the catalytic domain of peptidoglycan N-... -

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Basic information

Entry
Database: PDB / ID: 5jmu
TitleThe crystal structure of the catalytic domain of peptidoglycan N-acetylglucosamine deacetylase from Eubacterium rectale ATCC 33656
ComponentsPeptidoglycan N-acetylglucosamine deacetylase
KeywordsHYDROLASE / peptidoglycan N-acetylglucosamine deacetylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding / membrane
Similarity search - Function
: / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel ...: / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Peptidoglycan N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesAgathobacter rectalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsTan, K. / Gu, M. / Clancy, S. / Joachimiak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of the catalytic domain of peptidoglycan N-acetylglucosamine deacetylase from Eubacterium rectale ATCC 33656 (CASP target)
Authors: Tan, K. / Gu, M. / Clancy, S. / Joachimiak, A.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2254
Polymers25,0761
Non-polymers1493
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.495, 60.323, 79.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidoglycan N-acetylglucosamine deacetylase


Mass: 25076.014 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 247-496)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990) (bacteria)
Strain: ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990
Gene: EUBREC_2389 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: C4ZEZ9
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris:HCl, 1.8M MgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 22, 2016 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.54→33.42 Å / Num. obs: 33862 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 20.3
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.7 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data scaling
HKL-3000phasing
HKL-3000data reduction
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.54→33.42 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.19
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 1694 5.01 %random
Rwork0.1554 ---
obs0.157 33794 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.54→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 6 199 1906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161788
X-RAY DIFFRACTIONf_angle_d1.4822454
X-RAY DIFFRACTIONf_dihedral_angle_d13.965648
X-RAY DIFFRACTIONf_chiral_restr0.078279
X-RAY DIFFRACTIONf_plane_restr0.009326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5385-1.58380.23621200.24192559X-RAY DIFFRACTION96
1.5838-1.63490.26131540.21882603X-RAY DIFFRACTION99
1.6349-1.69340.22951500.20362638X-RAY DIFFRACTION100
1.6934-1.76120.26031200.18972656X-RAY DIFFRACTION100
1.7612-1.84130.22461540.18022640X-RAY DIFFRACTION100
1.8413-1.93840.19841400.1622678X-RAY DIFFRACTION100
1.9384-2.05980.19921480.15192635X-RAY DIFFRACTION100
2.0598-2.21880.16841510.14242683X-RAY DIFFRACTION100
2.2188-2.4420.17831250.14622713X-RAY DIFFRACTION100
2.442-2.79530.16371380.15462694X-RAY DIFFRACTION100
2.7953-3.52110.16961330.14372756X-RAY DIFFRACTION100
3.5211-33.42840.17821610.13362845X-RAY DIFFRACTION100
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)
11.20370.26580.16582.34850.44511.10770.0028-0.17410.02230.0731-0.02150.0509-0.0518-0.04960.01110.09620.01060.00050.11330.01440.080539.942142.518219.518
20.62660.15120.15021.0763-0.73532.5914-0.01060.0190.11790.02480.03580.0066-0.12460.0322-0.02070.1049-0.00090.00450.1092-0.00530.144745.224852.88177.737
33.12670.3018-0.82710.74250.39881.89820.06790.03850.11760.0218-0.0210.145-0.0104-0.2024-0.03480.11280.0178-0.01070.11110.03130.126430.403840.911211.4482
41.52760.0641-0.08171.7627-1.38571.202-0.0583-0.1027-0.0277-0.04890.0520.06530.1234-0.06940.00030.0994-0.0207-0.01350.0908-0.0230.092134.414936.748114.0158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 277 through 338 )
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 412 )
3X-RAY DIFFRACTION3chain 'A' and (resid 413 through 459 )
4X-RAY DIFFRACTION4chain 'A' and (resid 460 through 496 )

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