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- PDB-3wx7: Crystal structure of COD -

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Basic information

Entry
Database: PDB / ID: 3wx7
TitleCrystal structure of COD
ComponentsChitin oligosaccharide deacetylase
KeywordsHYDROLASE / oligosaccharide deacetylace / carbohydrate-binding
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 / metal ion binding
Similarity search - Function
Seminal Fluid Protein PDC-109 (Domain B) - #90 / : / Glycoside hydrolase/deacetylase / Carbohydrate-binding module family 5/12 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 ...Seminal Fluid Protein PDC-109 (Domain B) - #90 / : / Glycoside hydrolase/deacetylase / Carbohydrate-binding module family 5/12 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Chitin-binding domain type 3 / Seminal Fluid Protein PDC-109 (Domain B) / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Ribbon / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chitin oligosaccharide deacetylase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.349 Å
AuthorsPark, S.-Y. / Sugiyama, K. / Hirano, T. / Nishio, T.
CitationJournal: FEBS Lett. / Year: 2015
Title: Structure-based analysis of domain function of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus.
Authors: Hirano, T. / Sugiyama, K. / Sakaki, Y. / Hakamata, W. / Park, S.Y. / Nishio, T.
History
DepositionJul 18, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 30, 2024Group: 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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: Chitin oligosaccharide deacetylase
B: Chitin oligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,50712
Polymers88,8092
Non-polymers69710
Water22,2851237
1
A: Chitin oligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7536
Polymers44,4051
Non-polymers3495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitin oligosaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7536
Polymers44,4051
Non-polymers3495
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.819, 104.106, 140.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Chitin oligosaccharide deacetylase / Chitin oligosaccharide deacetylase COD1


Mass: 44404.656 Da / Num. of mol.: 2 / Fragment: UNP residues 26-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: KN1699 / Gene: cod1, COD / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6P4T5

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Non-polymers , 5 types, 1247 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1237 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.54 Å3/Da / Density % sol: 51.63 % / Mosaicity: 0.311 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Tris-HCl, 10% PEG8K, 0.2M MgCl2, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.98
SYNCHROTRONPhoton Factory BL-17A21.28275
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 6, 2011
ADSC QUANTUM 3152CCDJul 6, 2011
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21.282751
ReflectionRedundancy: 7.7 % / Number: 826548 / Rmerge(I) obs: 0.055 / Χ2: 2.87 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 107972 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.485010.0382.7619.2
3.554.4810.0433.48.8
3.113.5510.0513.8928.9
2.823.1110.0533.6318.9
2.622.8210.0553.3168.9
2.462.6210.0583.2668.8
2.342.4610.0613.1588.7
2.242.3410.0633.1088.6
2.152.2410.0683.0948.5
2.082.1510.0742.9628.4
2.012.0810.082.8678.3
1.962.0110.0872.7638.1
1.91.9610.0982.5448
1.861.910.1132.3997.8
1.821.8610.1242.1477.7
1.781.8210.1372.0726.7
1.741.7810.1421.8585.2
1.711.7410.1531.5924.4
1.681.7110.1581.5183.9
1.651.6810.1731.4183.4
ReflectionResolution: 1.349→50 Å / Num. obs: 195977 / % possible obs: 98.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 11.46 Å2 / Rmerge(I) obs: 0.049 / Χ2: 1.841 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1,2 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.35-1.372.80.21188450.93189.5
1.37-1.43.40.20791930.99793.8
1.4-1.434.20.20596181.02897.8
1.43-1.454.40.18796851.04698.3
1.45-1.494.60.16897171.12198.5
1.49-1.524.80.14897901.17498.8
1.52-1.564.90.13297381.24399
1.56-1.65.10.11998041.32799.1
1.6-1.655.30.11197891.4199.2
1.65-1.75.50.09698541.4999.5
1.7-1.765.60.08698641.55799.6
1.76-1.835.90.07798761.69899.7
1.83-1.926.10.06998691.81499.8
1.92-2.026.30.05999441.94999.7
2.02-2.146.50.05499092.08899.9
2.14-2.316.70.05399752.38699.9
2.31-2.546.70.05799932.94299.9
2.54-2.916.70.052100553.07199.8
2.91-3.666.70.038101162.53699.8
3.66-506.90.031103431.98998.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.349→48.806 Å / FOM work R set: 0.9003 / SU ML: 0.12 / σ(F): 1.5 / Phase error: 17.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1976 9869 5.04 %
Rwork0.1738 --
obs0.175 195924 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.95 Å2 / Biso mean: 16.16 Å2 / Biso min: 5.49 Å2
Refinement stepCycle: LAST / Resolution: 1.349→48.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 36 1237 7543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066482
X-RAY DIFFRACTIONf_angle_d1.0828870
X-RAY DIFFRACTIONf_chiral_restr0.044958
X-RAY DIFFRACTIONf_plane_restr0.0061174
X-RAY DIFFRACTIONf_dihedral_angle_d11.4542246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3492-1.36450.27223050.22895420572587
1.3645-1.38060.2463100.22685665597591
1.3806-1.39740.23823220.21865874619695
1.3974-1.41510.22593300.21076103643398
1.4151-1.43370.24143230.20526118644198
1.4337-1.45340.23413210.19946116643798
1.4534-1.47410.21183210.19646210653199
1.4741-1.49610.21433390.18826129646899
1.4961-1.51950.17283640.17886158652299
1.5195-1.54440.20533120.17366195650799
1.5444-1.5710.19532980.17556251654999
1.571-1.59960.18553300.17246187651799
1.5996-1.63040.19953420.17416177651999
1.6304-1.66370.2033340.16846218655299
1.6637-1.69980.20543090.172862636572100
1.6998-1.73940.20773290.176562266555100
1.7394-1.78290.2083240.174462986622100
1.7829-1.83110.18893200.171662556575100
1.8311-1.8850.20093250.177162566581100
1.885-1.94580.20133610.17662816642100
1.9458-2.01540.18793340.167862656599100
2.0154-2.09610.19172960.167763176613100
2.0961-2.19150.19093080.169563336641100
2.1915-2.3070.19153260.170263216647100
2.307-2.45150.20683520.175563046656100
2.4515-2.64080.19543560.185363456701100
2.6408-2.90650.20253510.178763436694100
2.9065-3.3270.20143380.174363996737100
3.327-4.19130.17663080.153364816789100
4.1913-48.83760.18283810.15976547692898

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