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- PDB-4wcj: Structure of IcaB from Ammonifex degensii -

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Basic information

Entry
Database: PDB / ID: 4wcj
TitleStructure of IcaB from Ammonifex degensii
ComponentsPolysaccharide deacetylase
KeywordsHYDROLASE / deacetylase / beta alpha barrel / carbohydrate binding / family 4 carbohydrate esterase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase/deacetylase / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Polysaccharide deacetylase
Similarity search - Component
Biological speciesAmmonifex degensii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLittle, D.J. / Bamford, N.C. / Pokrovskaya, V. / Robinson, H. / Nitz, M. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)43998 Canada
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for the De-N-acetylation of Poly-beta-1,6-N-acetyl-d-glucosamine in Gram-positive Bacteria.
Authors: Little, D.J. / Bamford, N.C. / Pokrovskaya, V. / Robinson, H. / Nitz, M. / Howell, P.L.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polysaccharide deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8743
Polymers29,7731
Non-polymers1012
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.686, 84.686, 71.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Polysaccharide deacetylase


Mass: 29773.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Loop (residues 50-64) was deleted from the construct
Source: (gene. exp.) Ammonifex degensii (bacteria) / Strain: DSM 10501 / KC4 / Gene: Adeg_0846 / Plasmid: pET28A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C9RCK9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43 % / Description: small octahedron
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 28% PEG MME 2000, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28034 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 60.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1760) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F9D

4f9d


Resolution: 1.7→33.512 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2002 7.14 %Random
Rwork0.2037 ---
obs0.2056 28021 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→33.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 2 132 1995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061915
X-RAY DIFFRACTIONf_angle_d1.0852603
X-RAY DIFFRACTIONf_dihedral_angle_d13.288686
X-RAY DIFFRACTIONf_chiral_restr0.04281
X-RAY DIFFRACTIONf_plane_restr0.006333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6992-1.74170.34351430.31961841X-RAY DIFFRACTION100
1.7417-1.78880.36211460.31121853X-RAY DIFFRACTION100
1.7888-1.84140.30291400.30021878X-RAY DIFFRACTION100
1.8414-1.90080.3111380.29261832X-RAY DIFFRACTION100
1.9008-1.96880.26541410.28011839X-RAY DIFFRACTION100
1.9688-2.04760.29661430.27431856X-RAY DIFFRACTION100
2.0476-2.14080.25811450.26371840X-RAY DIFFRACTION100
2.1408-2.25360.31181390.24881870X-RAY DIFFRACTION100
2.2536-2.39480.26661470.24361850X-RAY DIFFRACTION100
2.3948-2.57960.28021390.23711858X-RAY DIFFRACTION100
2.5796-2.83910.26351400.21881867X-RAY DIFFRACTION100
2.8391-3.24960.22161440.20551864X-RAY DIFFRACTION100
3.2496-4.0930.2111500.1611876X-RAY DIFFRACTION100
4.093-33.51890.16081470.14531895X-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)
13.18440.6413-1.7040.3657-0.79241.7793-0.1454-0.2259-0.90071.4727-0.0129-0.7940.15830.38320.07630.93870.1228-0.21390.2856-0.02650.5426175.472818.365579.251
23.08170.78150.12091.29921.61232.5069-0.3343-0.0714-0.47981.79080.69290.53090.3572-0.22480.39170.95720.2290.3320.28030.02790.448160.460121.162775.057
30.75240.3088-0.28720.6006-0.05010.8498-0.1624-0.22380.13241.84250.6031-0.8498-0.2114-0.15070.6721.15730.2149-0.45490.148-0.33230.4464178.164729.144478.283
48.1095-2.2751-4.4483.23543.20643.942-0.33650.06170.04410.94540.24050.87780.0621-0.39470.17530.4490.06780.16610.23280.01890.314159.636530.621969.1113
55.5931-0.3163-0.79622.09421.02044.3888-0.12210.3348-0.0990.52590.35620.00960.2920.1834-0.1930.3661-0.02980.02560.1322-0.01140.1839166.960427.924162.7404
65.80654.84974.93534.6575.33946.6932-0.21590.37890.23050.26610.12680.5551-0.2063-0.15220.07360.26250.0050.06160.27660.02040.2301163.448533.676361.0809
71.0448-0.96660.98949.00360.86973.9098-0.09080.5391-0.6074-0.32480.1404-0.09330.46840.30720.01720.255-0.04770.08570.3848-0.21020.4572173.968620.003157.2049
82.5608-3.8629-1.0456.44451.04242.45550.01621.028-0.2562-0.84210.014-0.68970.14190.0331-0.16570.317-0.10720.16430.4986-0.22260.5255179.999325.724652.186
92.4999-2.5861-0.66383.8062-0.61512.1345-0.12430.05260.15810.21860.0658-0.8667-0.20150.11930.05690.2853-0.0079-0.0550.2807-0.13510.4923183.274824.683762.2006
104.77980.62690.16291.5681-0.30142.0637-0.2315-0.2029-0.67761.53660.3515-0.85410.09540.0927-0.02280.7860.1411-0.16940.2347-0.06490.5537176.026217.590477.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 149 )
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 187 )
8X-RAY DIFFRACTION8chain 'A' and (resid 188 through 213 )
9X-RAY DIFFRACTION9chain 'A' and (resid 214 through 245 )
10X-RAY DIFFRACTION10chain 'A' and (resid 246 through 278 )

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