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- PDB-8yh4: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) ... -

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Basic information

Entry
Database: PDB / ID: 8yh4
TitleChito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with chitosanbiose (GlcN)2
ComponentsNodB homology domain-containing protein
KeywordsHYDROLASE / Vibrio campbellii / Chito oligosaccharide deacetylase / Deacetylase Enzyme / CE4 family member
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / NodB homology domain profile. / Carbohydrate-binding module family 5/12 / NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase/deacetylase, beta/alpha-barrel
Similarity search - Domain/homology
NodB homology domain-containing protein
Similarity search - Component
Biological speciesVibrio campbellii ATCC BAA-1116 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.128 Å
AuthorsSirikan, P. / Tamo, F. / Robinson, R.C. / Wipa, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To be published
Title: Chito oligosaccharide deacetylase from vibrio campbellii (VhCOD) in complex with chitosanbiose (GlcN)2
Authors: Sirikan, P. / Wipa, S. / Tamo, F. / Robinson, R.C.
History
DepositionFeb 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NodB homology domain-containing protein
B: NodB homology domain-containing protein
C: NodB homology domain-containing protein
D: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,87519
Polymers178,0924
Non-polymers1,78415
Water25,2211400
1
A: NodB homology domain-containing protein
B: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9269
Polymers89,0462
Non-polymers8807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-116 kcal/mol
Surface area29940 Å2
MethodPISA
2
C: NodB homology domain-containing protein
D: NodB homology domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,94910
Polymers89,0462
Non-polymers9038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-126 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.894, 118.458, 252.574
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
NodB homology domain-containing protein / Chito oligosaccharide deacetylase


Mass: 44522.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio campbellii ATCC BAA-1116 (bacteria)
Gene: VIBHAR_03626 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: A7MSF4
#2: Polysaccharide
2-amino-2-deoxy-beta-D-glucopyranose-(1-4)-2-amino-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 340.327 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNb1-4DGlcpNb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*N]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+1)][b-D-GlcpN]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1400 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium fluoride, 0.1M Bis-Tris propane pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.90003 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90003 Å / Relative weight: 1
ReflectionResolution: 2.128→50 Å / Num. obs: 5768039 / % possible obs: 99.6 % / Redundancy: 7.2 % / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.091 / Rrim(I) all: 0.231 / Net I/σ(I): 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.13-2.176.30.2150900.9730.9930.090.2290.86599.3
2.17-2.216.70.18350240.9810.9950.0760.1980.88998.9
2.21-2.256.90.16151010.9860.9970.0660.1740.86399.5
2.25-2.297.10.15450520.9880.9970.0620.1660.89999.2
2.29-2.347.10.13551080.990.9980.0540.1450.89299.1
2.34-2.47.20.11950530.9920.9980.0470.1280.871100
2.4-2.467.30.10550960.9940.9980.0410.1130.87699.3
2.46-2.537.30.09751280.9940.9990.0380.1040.86499.9
2.53-2.67.40.08450790.9950.9990.0330.090.86699.5
2.6-2.687.40.07151220.9960.9990.0280.0760.8599.6
2.68-2.787.40.06351450.9960.9990.0240.0670.86899.7
2.78-2.897.40.05251540.9970.9990.020.0560.891100
2.89-3.027.40.04451190.99810.0170.0480.90399.8
3.02-3.187.40.03651520.99810.0140.0390.85599.9
3.18-3.387.40.02951860.99910.0110.0310.77199.9
3.38-3.647.40.02451630.99910.0090.0250.76199.9
3.64-4.017.30.02352270.99910.0090.0240.83699.9
4.01-4.597.30.0252440.99910.0080.0210.79999.8
4.59-5.787.20.01852970.99910.0070.0190.62399.9
5.78-506.80.01754760.99910.0070.0190.63798.2

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Processing

Software
NameVersionClassification
PHENIX(1.18.2-3874-000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.128→24.887 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1824 8524 4.96 %
Rwork0.1507 --
obs0.1523 171802 86.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.128→24.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12551 0 103 1400 14054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213027
X-RAY DIFFRACTIONf_angle_d0.55317894
X-RAY DIFFRACTIONf_dihedral_angle_d11.6287523
X-RAY DIFFRACTIONf_chiral_restr0.0441972
X-RAY DIFFRACTIONf_plane_restr0.0042339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1281-2.15230.22071730.17773175X-RAY DIFFRACTION50
2.1523-2.17760.18721730.16733321X-RAY DIFFRACTION53
2.1776-2.20420.15781620.15783421X-RAY DIFFRACTION55
2.2042-2.2320.20651680.16023628X-RAY DIFFRACTION57
2.232-2.26140.18131800.15663722X-RAY DIFFRACTION59
2.2614-2.29240.20442190.15073922X-RAY DIFFRACTION63
2.2924-2.32510.18492250.14594205X-RAY DIFFRACTION67
2.3251-2.35980.20342350.14774440X-RAY DIFFRACTION71
2.3598-2.39660.1742350.14434750X-RAY DIFFRACTION76
2.3966-2.43590.20112620.14715161X-RAY DIFFRACTION82
2.4359-2.47780.19373190.15365436X-RAY DIFFRACTION88
2.4778-2.52280.19842840.15555847X-RAY DIFFRACTION93
2.5228-2.57130.19333580.15655932X-RAY DIFFRACTION95
2.5713-2.62380.21113400.15876207X-RAY DIFFRACTION99
2.6238-2.68070.19962900.15726218X-RAY DIFFRACTION99
2.6807-2.7430.21423680.16746271X-RAY DIFFRACTION100
2.743-2.81150.19543000.16366208X-RAY DIFFRACTION100
2.8115-2.88740.20253230.1666360X-RAY DIFFRACTION100
2.8874-2.97230.18293110.17496192X-RAY DIFFRACTION100
2.9723-3.0680.21093630.17616210X-RAY DIFFRACTION100
3.068-3.17750.20213200.1676294X-RAY DIFFRACTION100
3.1775-3.30440.19243200.16446258X-RAY DIFFRACTION100
3.3044-3.45440.18863320.15416230X-RAY DIFFRACTION100
3.4544-3.63610.18162830.1426310X-RAY DIFFRACTION100
3.6361-3.86310.15053140.1376305X-RAY DIFFRACTION100
3.8631-4.16010.16233490.13116230X-RAY DIFFRACTION100
4.1601-4.57640.16713360.126266X-RAY DIFFRACTION100
4.5764-5.23320.1462900.12716272X-RAY DIFFRACTION100
5.2332-6.57320.18143600.15666242X-RAY DIFFRACTION100
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)
11.6025-0.12680.04841.2561-0.06371.32320.0217-0.2062-0.06920.32860.017-0.01170.00290.0120.00650.1699-0.0159-0.0330.07760.04480.119413.3679-16.7869-42.9261
20.8512-0.6958-0.03621.77930.49410.17750.0785-0.6419-0.46240.984-0.1519-0.09370.1693-0.05230.0390.4012-0.1119-0.09360.31410.20770.312510.1518-28.2478-42.0016
30.90490.07020.20710.97720.0930.34470.04020.0025-0.21880.04620.02050.01180.1513-0.02030.00260.1194-0.0066-0.02210.09970.00870.16619.2881-23.7249-57.5851
40.56330.44050.02561.34181.00760.985-0.05960.00390.2604-0.2295-0.10890.6687-0.2664-0.3023-0.03450.10390.0265-0.02030.17750.00930.3271-7.47141.7282-62.142
50.51110.1613-0.01850.57690.26630.16710.02910.07630.163-0.0758-0.02080.1635-0.1048-0.0944-0.00040.12740.02350.00510.107-0.01750.17311.739121.9431-53.6659
60.37080.06210.08310.3247-0.03630.11120.0184-0.27770.06430.27830.01310.1819-0.1158-0.1006-0.00220.1778-0.01390.01180.1477-0.01080.116712.710515.0173-43.642
70.5157-0.1384-0.08060.3748-0.02490.04340.0184-0.4411-0.0440.42380.083-0.07130.03180.01040.03520.2556-0.0176-0.07760.25540.00150.171924.062810.2845-39.3552
80.2464-0.0910.03440.0488-0.03030.0592-0.0536-0.1994-0.20950.102-0.0021-0.00370.0376-0.0053-0.00140.1442-0.0111-0.0290.13440.00970.185516.36189.6622-54.4673
90.1997-0.1359-0.45830.54480.23281.8975-0.019-0.16620.08390.14160.0524-0.3353-0.21410.5357-0.00190.144-0.0112-0.08550.1936-0.02520.281936.11413.8159-51.1851
100.6554-0.1015-0.42860.2989-0.40991.05420.1479-0.3460.32780.511-0.0552-0.3329-0.37780.17620.07760.2784-0.0572-0.03050.2326-0.08120.252423.821326.5431-51.0454
110.64860.20190.230.5434-0.25890.3753-0.01680.02230.19950.06210.0266-0.1376-0.17750.02-0.00210.1999-0.0096-0.01530.1007-0.02260.205921.083628.1409-57.3756
120.20260.0626-0.1670.20090.12680.2792-0.01190.05110.0394-0.1076-0.0182-0.0149-0.0632-0.0732-00.13390.0054-0.03680.1137-0.00020.135617.43555.1496-72.2821
130.47050.31570.10210.9549-0.44580.3855-0.03980.0747-0.1373-0.19690.0245-0.33580.16770.1756-0.01370.11090.0186-0.010.1103-0.00810.234435.315-8.882-67.9587
140.6836-0.07270.13260.63860.16990.2464-0.04970.04780.16090.05590.0535-0.2497-0.37090.20360.00680.2622-0.102-0.04960.1926-0.02180.165326.531519.487-111.2937
150.6072-0.46340.43671.3001-0.03390.4251-0.08910.46940.1833-0.4204-0.0243-0.1659-0.20580.2431-0.04080.3234-0.0595-0.02590.30560.02620.129518.115417.0577-126.0076
160.47690.3188-0.01820.4047-0.20310.21870.02870.1561-0.1631-0.04210.002-0.1524-0.13180.1388-0.07020.2053-0.0198-0.03550.1825-0.06470.116620.59959.8033-111.0088
170.36820.5498-0.39310.8685-0.49780.9257-0.12150.17540.2536-0.12440.18140.3049-0.3506-0.42390.10120.2776-0.0038-0.07620.2408-0.01310.21143.191117.9246-117.4803
182.3497-0.8889-1.2230.3620.61721.51130.05030.26440.6491-0.28780.0862-0.0012-0.7950.01720.54470.5255-0.0159-0.11060.23170.03330.291615.444427.7531-109.1985
190.568-0.33340.17240.2999-0.0280.5569-0.0907-0.06890.16090.16150.064-0.0193-0.3887-0.03530.00050.3114-0.0098-0.05670.1671-0.03320.150615.806918.2021-99.9003
200.28950.0625-0.16060.1490.08540.2807-0.0195-0.01-0.24990.0119-0.1026-0.00570.03410.2048-0.05080.1271-0.0112-0.03180.1728-0.02140.180511.3715-7.4748-101.3875
210.1313-0.0051-0.05610.06130.01510.23760.00540.2063-0.4026-0.0872-0.0120.21940.2343-0.4685-0.00240.1737-0.0155-0.01630.2981-0.06730.2809-1.8663-9.2652-112.3592
220.6160.10050.01950.3978-0.00920.2717-0.02630.366-0.3129-0.26030.03340.12980.15130.0411-0.09270.1594-0.0475-0.06330.3604-0.190.283216.4461-15.1603-133.8911
230.56190.2171-0.02680.7862-0.0090.2939-0.05780.3753-0.0223-0.1950.1381-0.0339-0.10610.11520.0510.1913-0.04660.02190.352-0.10040.18129.0344-6.6266-130.91
240.61360.2686-0.17740.736-0.61481.2717-0.12580.2906-0.2361-0.0744-0.0046-0.2610.06770.3231-0.95070.145-0.060.02610.4372-0.19240.217542.2433-8.5856-126.5872
250.1313-0.23920.25531.7986-0.24980.60250.00270.8163-0.2443-0.575-0.1009-0.0480.11790.1663-0.27730.30570.00380.01160.6694-0.25880.341629.7532-20.7441-136.8952
260.30610.0846-0.16320.34670.03290.7476-0.14590.3319-0.3993-0.27560.0454-0.00490.14540.0179-0.71350.16180.01090.02630.3847-0.3650.370230.3689-24.6675-131.29
270.01250.01270.03630.17560.1110.1108-0.00540.1093-0.0675-0.20940.0195-0.0033-0.01550.00380.07170.2794-0.1199-0.01460.4282-0.64420.532317.7692-30.3939-138.3356
280.0282-0.0007-0.01420.12730.0930.0668-0.00010.0738-0.37810.15980.00510.05260.1918-0.0264-0.00220.1938-0.00350.01940.2157-0.05740.333122.011-21.8746-110.0484
290.0599-0.07180.02730.19420.09480.1554-0.04510.0264-0.07270.16090.15510.17140.1132-0.05760.01130.16520.00680.01730.2328-0.01460.234125.6663-12.3321-101.7821
300.0693-0.09090.02380.4237-0.12960.0422-0.0567-0.18210.06410.4684-0.036-0.262-0.21280.26040.00120.2073-0.0145-0.0210.3328-0.08110.235140.8786-4.023-101.2011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 195 )
2X-RAY DIFFRACTION2chain 'A' and (resid 196 through 223 )
3X-RAY DIFFRACTION3chain 'A' and (resid 224 through 365 )
4X-RAY DIFFRACTION4chain 'A' and (resid 366 through 405 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 79 )
7X-RAY DIFFRACTION7chain 'B' and (resid 80 through 123 )
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 150 )
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 196 )
10X-RAY DIFFRACTION10chain 'B' and (resid 197 through 223 )
11X-RAY DIFFRACTION11chain 'B' and (resid 224 through 298 )
12X-RAY DIFFRACTION12chain 'B' and (resid 299 through 365 )
13X-RAY DIFFRACTION13chain 'B' and (resid 366 through 405 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 80 )
15X-RAY DIFFRACTION15chain 'C' and (resid 81 through 123 )
16X-RAY DIFFRACTION16chain 'C' and (resid 124 through 150 )
17X-RAY DIFFRACTION17chain 'C' and (resid 151 through 196 )
18X-RAY DIFFRACTION18chain 'C' and (resid 197 through 223 )
19X-RAY DIFFRACTION19chain 'C' and (resid 224 through 339 )
20X-RAY DIFFRACTION20chain 'C' and (resid 340 through 365 )
21X-RAY DIFFRACTION21chain 'C' and (resid 366 through 405 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 63 )
23X-RAY DIFFRACTION23chain 'D' and (resid 64 through 170 )
24X-RAY DIFFRACTION24chain 'D' and (resid 171 through 196 )
25X-RAY DIFFRACTION25chain 'D' and (resid 197 through 223 )
26X-RAY DIFFRACTION26chain 'D' and (resid 224 through 280 )
27X-RAY DIFFRACTION27chain 'D' and (resid 281 through 298 )
28X-RAY DIFFRACTION28chain 'D' and (resid 299 through 339 )
29X-RAY DIFFRACTION29chain 'D' and (resid 340 through 365 )
30X-RAY DIFFRACTION30chain 'D' and (resid 366 through 405 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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