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- PDB-5nc6: Crystal structure of the polysaccharide deacetylase Bc1974 from B... -

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Basic information

Entry
Database: PDB / ID: 5nc6
TitleCrystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (E)-N-hydroxy-3-(naphthalen-1-yl)prop-2-enamide
Components(Peptidoglycan N-acetylglucosamine ...) x 2
KeywordsHYDROLASE / CE4 fold / polysaccharide deacetylase / Bacillus cereus / PgdA / hydroxamate ligand
Function / homology
Function and homology information


peptidoglycan-N-acetylglucosamine deacetylase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / membrane / metal ion binding / plasma membrane
Similarity search - Function
NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
3-naphthalen-1-yl-~{N}-oxidanyl-propanamide / ACETATE ION / TRIETHYLENE GLYCOL / Peptidoglycan-N-acetylglucosamine deacetylase / Peptidoglycan-N-acetylglucosamine deacetylase BC_1974
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGiastas, P. / Andreou, A. / Balomenou, S. / Bouriotis, V. / Eliopoulos, E.E.
CitationJournal: Biochemistry / Year: 2018
Title: Structures of the Peptidoglycan N-Acetylglucosamine Deacetylase Bc1974 and Its Complexes with Zinc Metalloenzyme Inhibitors.
Authors: Giastas, P. / Andreou, A. / Papakyriakou, A. / Koutsioulis, D. / Balomenou, S. / Tzartos, S.J. / Bouriotis, V. / Eliopoulos, E.E.
History
DepositionMar 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidoglycan N-acetylglucosamine deacetylase
B: Peptidoglycan N-acetylglucosamine deacetylase
C: Peptidoglycan N-acetylglucosamine deacetylase
D: Peptidoglycan N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,43114
Polymers115,4084
Non-polymers1,02210
Water1,58588
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-120 kcal/mol
Surface area32110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.358, 118.012, 98.618
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Peptidoglycan N-acetylglucosamine ... , 2 types, 4 molecules ABCD

#1: Protein Peptidoglycan N-acetylglucosamine deacetylase / Peptidoglycan-N-acetylglucosamine deacetylase / Polysaccharide deacetylase


Mass: 23250.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues of the N-terminus were not detected / Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A3VTA3, UniProt: Q81EJ6*PLUS
#2: Protein Peptidoglycan N-acetylglucosamine deacetylase / Peptidoglycan-N-acetylglucosamine deacetylase / Polysaccharide deacetylase


Mass: 30719.252 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: AT268_30040, B4155_0776, TQ94_03800, TU58_19865, WR51_09920, WR52_09510
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A3VTA3, UniProt: Q81EJ6*PLUS

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Non-polymers , 6 types, 98 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Details: Residues of the N-terminus were not detected / Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-8SQ / 3-naphthalen-1-yl-~{N}-oxidanyl-propanamide


Mass: 215.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 100 mM Na citrate, 10% ethanol, 30% 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: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.35 Å / Num. obs: 52715 / % possible obs: 99.46 % / Redundancy: 4.6 % / Biso Wilson estimate: 49.47 Å2 / Net I/σ(I): 1.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Num. unique obs: 2630 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.346 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 0.95 / Phase error: 33.85
RfactorNum. reflection% reflection
Rfree0.2801 2633 4.99 %
Rwork0.22 --
obs0.2234 52715 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6585 0 54 88 6727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156844
X-RAY DIFFRACTIONf_angle_d1.1789233
X-RAY DIFFRACTIONf_dihedral_angle_d4.7694440
X-RAY DIFFRACTIONf_chiral_restr0.056956
X-RAY DIFFRACTIONf_plane_restr0.0081204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.85120.42711270.38562302X-RAY DIFFRACTION86
2.8512-2.90610.37531420.35062748X-RAY DIFFRACTION99
2.9061-2.96540.41281370.32512562X-RAY DIFFRACTION99
2.9654-3.02980.38181410.31822644X-RAY DIFFRACTION99
3.0298-3.10030.41981420.32762717X-RAY DIFFRACTION100
3.1003-3.17780.32891350.29672598X-RAY DIFFRACTION100
3.1778-3.26370.40881410.26522681X-RAY DIFFRACTION100
3.2637-3.35970.33571400.25172671X-RAY DIFFRACTION100
3.3597-3.46810.32951410.2362664X-RAY DIFFRACTION99
3.4681-3.5920.27261410.22532643X-RAY DIFFRACTION99
3.592-3.73580.31321380.20992670X-RAY DIFFRACTION99
3.7358-3.90580.26551360.19812632X-RAY DIFFRACTION99
3.9058-4.11160.26311420.1792705X-RAY DIFFRACTION99
4.1116-4.3690.2951380.16742629X-RAY DIFFRACTION99
4.369-4.70610.21651380.16592642X-RAY DIFFRACTION99
4.7061-5.17910.23871370.17222619X-RAY DIFFRACTION98
5.1791-5.92730.25521400.18132647X-RAY DIFFRACTION98
5.9273-7.46310.21841370.20442636X-RAY DIFFRACTION100
7.4631-47.35280.22791400.20092672X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.0466-1.1542-0.27964.8619-2.45121.730.9066-0.2442-0.7238-1.5370.232-0.03391.18970.5612-0.57170.49070.05620.06410.733-0.14460.383419.4993-1.556588.7134
24.5665-0.4014-0.07495.759-0.30345.7013-0.09540.9146-0.4922-0.87380.465-0.10311.6040.8216-0.1870.69990.1325-0.06840.5968-0.15280.493819.5924-6.877184.2576
31.2173-0.201-1.13731.17571.40262.92160.36380.1209-0.3888-0.5788-0.0130.30370.6069-0.02770.321.0956-0.0072-0.22040.4299-0.04990.61979.3788-11.002489.4962
40.92090.84951.78221.65660.26645.81630.7276-0.3736-0.2445-0.08480.07180.19011.8852-0.0859-0.54090.6007-0.0206-0.05750.3866-0.05570.515211.8414-4.628101.6452
51.23960.18770.09551.6037-0.61821.8640.17920.0074-0.0687-0.5710.1510.11470.37620.1435-0.22960.48120.0632-0.06460.3479-0.06050.414718.06155.309100.0138
61.9858-0.45281.43864.5788-1.35154.33330.25130.23030.032-0.9781-0.1952-0.3239-0.67541.2662-0.06040.615-0.09280.12940.6837-0.11760.417524.23836.667485.7616
72.42810.3320.04030.9681-0.2631.54170.2010.6760.0179-0.29330.1511-1.16280.67781.3084-0.26450.63080.06610.09491.0155-0.32420.699727.6779-2.062686.1499
80.8989-0.411-1.21072.0376-0.75672.61990.21620.0487-0.70570.26560.131-0.52590.46021.3746-0.37830.46240.1201-0.19870.4891-0.12440.68726.61851.7145106.7702
92.50932.38831.90522.42561.48763.6279-0.23330.28170.17860.58180.2137-0.51820.95040.8732-0.01750.53270.1198-0.16870.5239-0.02480.556432.40125.065129.0888
102.7511.4335-0.77172.69910.19593.14010.3261-0.1032-0.4230.4377-0.08260.23850.53920.0902-0.2710.61470.0111-0.09530.37680.08070.41521.37825.4493136.086
110.12650.154-0.00972.8011-0.74640.22060.2341-0.1124-0.01860.9097-0.04260.1755-0.12710.0023-0.09931.1738-0.0256-0.09460.42880.06450.540419.85716.0236143.3602
124.62460.36510.51395.478-0.97012.0830.6343-0.36530.3390.32760.01061.72370.2723-0.7541-0.59560.7204-0.14870.12290.456-0.02480.560817.252221.3009144.8039
132.41380.1268-1.01632.31990.42751.96180.113-0.16370.0380.6091-0.1246-0.21580.3748-0.298-0.15340.4425-0.0544-0.09740.30590.03050.547725.274616.3854128.8991
140.09540.460.45882.7389-0.41653.6780.18660.01330.2287-0.168-0.1187-0.6039-0.01020.5106-0.0420.25250.0188-0.01230.4786-0.08040.549534.347213.9649124.0072
153.00272.014-3.69983.4149-2.15965.14150.357-0.8291-0.9831.8112-0.2719-1.2302-0.58850.87410.06920.69890.0199-0.30560.7204-0.05460.67838.88611.3104138.7384
163.02890.3631-0.45450.4143-0.256730.504-0.18310.63941.0896-0.1979-0.25320.09450.7842-0.36150.9846-0.0318-0.1740.4652-0.10030.530527.318522.2891144.7053
171.7072-0.8098-0.38842.77590.65813.7732-0.4091-0.21980.26560.5930.2488-0.4545-0.76140.14410.11170.70180.0141-0.06460.4504-0.05420.429128.132245.6723141.3872
182.3892-1.09920.40670.491-0.06451.4496-0.2833-0.23660.40080.6851-0.1039-0.0291-0.8935-0.2110.45180.76420.01550.02090.3591-0.03740.307223.548640.2159128.0996
192.6621-0.89921.7042.14680.31874.23610.00120.0787-0.15080.81420.1829-0.69130.49690.7504-0.24620.8130.0782-0.25840.5754-0.09970.729539.051634.6004142.3632
202.84810.35190.72452.69120.71742.607-0.10280.13220.4235-0.26880.4093-0.7113-0.5520.8026-0.10860.6732-0.10170.03110.5455-0.13840.558236.95142.3128128.1961
213.1997-1.2511-0.57952.53711.95182.52940.16190.5937-0.3109-1.45570.2316-0.1648-0.1663-0.281-0.05210.7202-0.22940.11810.50240.02350.411622.853527.886596.7664
221.1246-0.32011.18911.09640.54112.2819-0.54780.13850.4596-0.2490.0951-0.2572-1.33910.69660.12530.8946-0.2618-0.08730.49710.03940.352223.110637.6903102.166
232.66690.4169-1.56650.73760.44552.0484-0.15320.23860.23390.3208-0.11580.194-1.3787-0.01680.13411.15230.0067-0.1960.41750.05320.523513.360842.754102.5906
241.81930.34690.73373.68340.5684.47830.0445-0.3281-0.6832-0.667-0.62950.8126-1.31880.3807-0.0219-0.14730.07320.15520.49450.05970.5326.17128.8692102.7597
250.0884-0.0937-0.013.3211-0.3890.1182-0.37820.28090.291-1.00780.07590.4402-0.3454-0.32550.10980.80450.0113-0.16620.40920.01160.54145.73633.928296.567
264.2448-0.764-0.11585.3946-1.81387.54910.0639-0.2425-0.953-0.44890.78430.9416-0.4314-0.3569-0.59920.4517-0.0418-0.05680.30440.03070.54042.763518.738696.9426
271.72250.2791.62841.3540.11442.02820.14290.1246-0.2623-0.13730.1818-0.0717-0.37730.0812-0.32320.336-0.09650.12710.37850.00730.42422.944823.8199105.4076
280.3854-0.50610.55222.53850.78244.90080.17160.43110.1325-0.69990.3238-0.1276-1.44421.1118-0.51190.6388-0.1491-0.00770.5457-0.00660.51127.695329.357196.9836
294.83011.4732-0.68120.85750.94423.4518-0.55990.3397-0.3261-0.96070.1516-0.0162-0.5650.08470.43990.5963-0.1128-0.03280.4632-0.0650.3811.34417.69591.402
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 167 through 204 )
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 233 )
7X-RAY DIFFRACTION7chain 'A' and (resid 234 through 261 )
8X-RAY DIFFRACTION8chain 'A' and (resid 262 through 273 )
9X-RAY DIFFRACTION9chain 'B' and (resid 68 through 93 )
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 140 )
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 166 )
12X-RAY DIFFRACTION12chain 'B' and (resid 167 through 183 )
13X-RAY DIFFRACTION13chain 'B' and (resid 184 through 204 )
14X-RAY DIFFRACTION14chain 'B' and (resid 205 through 249 )
15X-RAY DIFFRACTION15chain 'B' and (resid 250 through 261 )
16X-RAY DIFFRACTION16chain 'B' and (resid 262 through 273 )
17X-RAY DIFFRACTION17chain 'C' and (resid 68 through 156 )
18X-RAY DIFFRACTION18chain 'C' and (resid 157 through 183 )
19X-RAY DIFFRACTION19chain 'C' and (resid 184 through 249 )
20X-RAY DIFFRACTION20chain 'C' and (resid 250 through 273 )
21X-RAY DIFFRACTION21chain 'D' and (resid 68 through 78 )
22X-RAY DIFFRACTION22chain 'D' and (resid 79 through 102 )
23X-RAY DIFFRACTION23chain 'D' and (resid 103 through 118 )
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 140 )
25X-RAY DIFFRACTION25chain 'D' and (resid 141 through 166 )
26X-RAY DIFFRACTION26chain 'D' and (resid 167 through 183 )
27X-RAY DIFFRACTION27chain 'D' and (resid 184 through 233 )
28X-RAY DIFFRACTION28chain 'D' and (resid 234 through 261 )
29X-RAY DIFFRACTION29chain 'D' and (resid 262 through 273 )

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