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- PDB-5nc9: Crystal structure of the polysaccharide deacetylase Bc1974 from B... -

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Basic information

Entry
Database: PDB / ID: 5nc9
TitleCrystal structure of the polysaccharide deacetylase Bc1974 from Bacillus cereus in complex with (2S)-2,6-diamino-N-hydroxyhexanamide
ComponentsPeptidoglycan N-acetylglucosamine deacetylase
KeywordsHYDROLASE / CE4 domain / polysaccharide deacetylase / PgdA / Bacillus cereus / 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 / 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
(2~{S})-2,6-bis(azanyl)-~{N}-oxidanyl-hexanamide / CITRIC ACID / TRIETHYLENE GLYCOL / Peptidoglycan-N-acetylglucosamine deacetylase BC_1974
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
Bacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsGiastas, P. / Andreou, A. / 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)112,85015
Polymers111,5394
Non-polymers1,31111
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-39 kcal/mol
Surface area32530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.767, 117.835, 99.059
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptidoglycan N-acetylglucosamine deacetylase


Mass: 27884.674 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_1974 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81EJ6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 113 molecules

#2: Chemical
ChemComp-8SZ / (2~{S})-2,6-bis(azanyl)-~{N}-oxidanyl-hexanamide


Mass: 161.202 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
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: 2.44→48.61 Å / Num. obs: 41046 / % possible obs: 98.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 45.71 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.44→2.53 Å / Num. unique obs: 3720 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→48.61 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 33.96
RfactorNum. reflection% reflection
Rfree0.279 3938 4.98 %
Rwork0.2198 --
obs0.2226 79064 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.44→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 75 102 6755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016866
X-RAY DIFFRACTIONf_angle_d1.189258
X-RAY DIFFRACTIONf_dihedral_angle_d14.4022510
X-RAY DIFFRACTIONf_chiral_restr0.047962
X-RAY DIFFRACTIONf_plane_restr0.0061207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4403-2.470.3715990.3751733X-RAY DIFFRACTION62
2.47-2.50130.38311410.34462725X-RAY DIFFRACTION98
2.5013-2.53420.33871440.33772693X-RAY DIFFRACTION99
2.5342-2.56890.41141450.33432774X-RAY DIFFRACTION99
2.5689-2.60560.47951470.33842794X-RAY DIFFRACTION99
2.6056-2.64450.38061380.33192695X-RAY DIFFRACTION98
2.6445-2.68580.31141430.3122713X-RAY DIFFRACTION99
2.6858-2.72990.41771470.29992803X-RAY DIFFRACTION99
2.7299-2.77690.31621430.27122735X-RAY DIFFRACTION99
2.7769-2.82740.3621450.29422719X-RAY DIFFRACTION99
2.8274-2.88180.34411410.28322771X-RAY DIFFRACTION99
2.8818-2.94060.37991450.28262754X-RAY DIFFRACTION99
2.9406-3.00460.28251400.26762693X-RAY DIFFRACTION98
3.0046-3.07440.35771430.2552750X-RAY DIFFRACTION98
3.0744-3.15130.27121380.2412689X-RAY DIFFRACTION98
3.1513-3.23650.34821390.23172715X-RAY DIFFRACTION98
3.2365-3.33170.34611440.22982736X-RAY DIFFRACTION98
3.3317-3.43920.26331440.21972664X-RAY DIFFRACTION97
3.4392-3.56210.30291440.21262749X-RAY DIFFRACTION97
3.5621-3.70470.29791340.20712647X-RAY DIFFRACTION98
3.7047-3.87320.22981430.1962758X-RAY DIFFRACTION97
3.8732-4.07730.23271430.1792685X-RAY DIFFRACTION98
4.0773-4.33260.20371430.17162666X-RAY DIFFRACTION97
4.3326-4.66690.23411360.17092676X-RAY DIFFRACTION96
4.6669-5.13610.22111420.17342733X-RAY DIFFRACTION98
5.1361-5.87820.24991430.18052671X-RAY DIFFRACTION97
5.8782-7.40170.23871410.19752699X-RAY DIFFRACTION96
7.4017-48.61960.23271430.18522686X-RAY DIFFRACTION97
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)
10.2416-0.4656-0.38453.3366-0.71842.06620.4866-0.4750.1704-0.29730.3175-0.69770.3930.9133-0.61540.77660.08420.02220.7462-0.25580.568524.6059-1.608891.4357
21.99860.74341.19462.31390.47581.93220.11150.2901-0.1838-0.16650.1177-0.051.13070.0011-0.19980.98680.0046-0.1740.4011-0.04120.525912.8855-6.228295.1176
31.82580.58660.35532.84130.71152.14510.05030.17630.0015-0.58280.1213-0.0050.30870.077-0.09380.4784-0.0001-0.08790.3107-0.06230.470118.10365.2307100.445
45.6665-0.6081-1.72967.5344-0.99675.0910.1414-0.65820.1749-1.2725-0.0294-0.4523-1.02461.88080.16111.0505-0.2480.13180.8957-0.08860.556524.03869.910981.4069
50.84840.21250.73232.248-0.32643.10370.27270.43410.1702-1.13250.192-0.5302-0.50450.9436-0.23910.9107-0.07760.07110.7398-0.2070.523924.77212.385685.5819
61.9984-0.4027-0.60560.2950.82842.53920.2440.6502-0.49010.31060.6666-0.41730.89941.0309-0.20330.91670.1727-0.12580.8889-0.40050.934430.0043-6.974693.6254
71.44340.1789-0.61181.3231-0.92683.18160.4698-0.172-0.85450.4388-0.0592-0.73390.78250.966-0.31960.67650.1311-0.25280.4768-0.13070.60626.55161.5562107.2066
80.34930.9030.45062.58530.80122.6944-0.6906-0.29550.58140.40370.234-0.14470.14690.52490.13510.54730.0652-0.21780.5371-0.04520.572533.060511.9614133.8639
91.62341.16490.47023.28741.19254.16280.23320.4639-0.39260.18670.1767-0.34471.00210.7959-0.43680.80350.1772-0.16430.5238-0.12590.544731.23092.2284129.6839
104.9979-0.3575-1.12332.59921.72913.33560.4265-0.3964-1.1880.154-0.3187-0.02350.90310.5502-0.00870.95370.1487-0.21880.45610.08740.59423.6112-2.884134.7745
111.00890.29730.96863.0241-0.67262.0363-0.08370.0523-0.07591.02620.17590.3650.1185-0.0974-0.10190.9135-0.0202-0.08310.41030.05490.447316.45048.7055141.1143
123.3892-1.0569-1.21894.39140.3530.45410.4807-0.29570.20620.7228-0.1687-0.71340.661-0.0901-0.42120.89210.0335-0.15730.4240.01730.477821.022314.8269141.1473
133.5957-3.83343.42868.4992-0.59985.40750.6505-1.66420.04460.67530.5830.6576-0.1197-0.6084-0.94571.01430.02150.07090.61760.06580.471917.209219.9194150.6938
141.69270.1315-0.09390.84310.60960.4454-0.0117-0.1375-0.03480.0791-0.16080.0160.2251-0.13490.17970.7188-0.0108-0.1620.33910.02540.530125.355116.3572128.7251
150.88360.52760.17663.17010.34183.03080.172-0.0617-0.10240.65910.0629-0.72850.14880.5689-0.15830.52510.0029-0.1180.443-0.09950.590633.69815.1319131.5893
161.94410.83830.53381.8742-0.94161.0106-0.33470.228-0.3842-0.39530.2291-0.38520.06960.04550.09760.7331-0.0206-0.27490.6441-0.1330.672838.580941.5761138.2116
171.4781-0.87580.89991.92890.27814.273-0.3585-0.46850.46151.00980.2524-0.6262-0.23040.9710.00290.95-0.0306-0.24290.661-0.11250.679936.610346.3711147.6034
184.70760.41831.21491.9390.61082.0792-0.3328-0.21940.32820.58410.3847-0.1765-0.54890.0968-0.10881.1969-0.016-0.17250.5354-0.07440.610526.500451.0418147.7968
192.2815-1.2542-0.44092.32641.16622.9953-0.2702-0.03310.15380.36530.1123-0.1688-0.8014-0.23030.19550.8279-0.0165-0.05420.3819-0.0760.373322.053944.5976136.2934
202.210.02750.26212.4334-0.1421.5331-0.3499-0.17290.00550.68890.2495-0.301-0.48820.2040.09710.9619-0.003-0.0420.3986-0.04430.405728.220434.7387134.2092
214.22870.3366-1.14593.9392-1.41962.07490.14650.382-0.05610.98660.1866-0.72940.22171.0882-0.20811.00060.1849-0.42890.7763-0.23280.894243.621830.0853146.9131
220.95250.48051.01671.16120.39213.92130.0386-0.1127-0.3850.46910.2948-0.96180.07541.0834-0.24570.80150.0464-0.29710.7132-0.19130.800741.92237.5212142.8133
231.01510.6199-0.01384.24090.51091.8036-0.31340.08760.325-0.83330.3177-0.8507-0.57370.81010.11030.7758-0.18450.0850.5415-0.10070.562836.853742.3021128.6252
245.1093-3.0506-2.59884.68663.8585.2429-0.36020.9454-0.2833-0.7927-0.21770.0313-0.3549-0.16320.5340.9816-0.24080.06690.50620.00860.452622.878227.898297.1924
253.7562-0.03390.29633.62880.82172.3978-0.15320.18190.2559-0.55250.08870.1312-0.9480.20260.07851.0026-0.0797-0.12160.37850.02890.363614.635735.7675102.8116
260.0398-0.28980.05932.9242-1.43310.6688-0.180.00630.2959-0.811-0.12480.5177-0.6061-0.14430.20171.19870.0428-0.27160.3957-0.00790.60795.904333.963496.9488
273.72490.2222-1.07125.16480.12135.288-0.36470.0735-0.6768-0.66540.29251.01580.0766-0.81830.05760.64680.0469-0.13160.3852-0.04960.56122.840618.871297.4351
282.2019-0.00910.24941.07260.11542.0784-0.0378-0.20570.3301-0.5232-0.11010.22740.1898-0.18060.00980.4984-0.06270.0390.31270.02660.415118.418323.6193106.1424
291.3484-0.03160.42141.19890.14460.29650.33350.4445-0.3883-0.49640.0063-0.2228-0.20560.45640.3668-0.406-0.16880.59520.6149-0.10810.186326.928323.9661105.5427
301.4171.12440.40872.2584-0.88723.4075-0.20950.76220.1194-0.51750.246-0.563-0.09480.54860.06010.501-0.23920.09680.6331-0.05930.586431.772829.7725104.693
312.0761-0.99711.15360.99260.41562.1231-0.14680.3146-0.0265-0.9711-0.0382-0.0085-0.41960.34130.00241.0365-0.1163-0.07690.507-0.02870.477517.584523.48490.7494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 68 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 166 )
3X-RAY DIFFRACTION3chain 'A' and (resid 167 through 204 )
4X-RAY DIFFRACTION4chain 'A' and (resid 205 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 261 )
7X-RAY DIFFRACTION7chain 'A' and (resid 262 through 273 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 78 )
9X-RAY DIFFRACTION9chain 'B' and (resid 79 through 102 )
10X-RAY DIFFRACTION10chain 'B' and (resid 103 through 119 )
11X-RAY DIFFRACTION11chain 'B' and (resid 120 through 156 )
12X-RAY DIFFRACTION12chain 'B' and (resid 157 through 174 )
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 204 )
15X-RAY DIFFRACTION15chain 'B' and (resid 205 through 273 )
16X-RAY DIFFRACTION16chain 'C' and (resid 68 through 78 )
17X-RAY DIFFRACTION17chain 'C' and (resid 79 through 102 )
18X-RAY DIFFRACTION18chain 'C' and (resid 103 through 118 )
19X-RAY DIFFRACTION19chain 'C' and (resid 119 through 166 )
20X-RAY DIFFRACTION20chain 'C' and (resid 167 through 204 )
21X-RAY DIFFRACTION21chain 'C' and (resid 205 through 219 )
22X-RAY DIFFRACTION22chain 'C' and (resid 220 through 249 )
23X-RAY DIFFRACTION23chain 'C' and (resid 250 through 273 )
24X-RAY DIFFRACTION24chain 'D' and (resid 68 through 78 )
25X-RAY DIFFRACTION25chain 'D' and (resid 79 through 140 )
26X-RAY DIFFRACTION26chain 'D' and (resid 141 through 166 )
27X-RAY DIFFRACTION27chain 'D' and (resid 167 through 183 )
28X-RAY DIFFRACTION28chain 'D' and (resid 184 through 204 )
29X-RAY DIFFRACTION29chain 'D' and (resid 205 through 233 )
30X-RAY DIFFRACTION30chain 'D' and (resid 234 through 249 )
31X-RAY DIFFRACTION31chain 'D' and (resid 250 through 273 )

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