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- PDB-1ods: Cephalosporin C deacetylase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1ods
TitleCephalosporin C deacetylase from Bacillus subtilis
ComponentsCEPHALOSPORIN C DEACETYLASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / ACETYLXYLAN / CARBOHYDRATE ESTERASE / CEPHALOSPORIN
Function / homology
Function and homology information


cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / acetylxylan esterase / acetylxylan esterase activity / polysaccharide metabolic process / carboxylic ester hydrolase activity / cellulose catabolic process / cytoplasm
Similarity search - Function
Acetyl xylan esterase / Carbohydrate esterase 7 family / Acetyl xylan esterase (AXE1) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsVincent, F. / Charnock, S.J. / Verschueren, K.H.G. / Turkenburg, J.P. / Scott, D.J. / Offen, W.A. / Roberts, S. / Pell, G. / Gilbert, H.J. / Brannigan, J.A. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Multifunctional Xylooligosaccharide/Cephalosporin C Deacetylase Revealed by the Hexameric Structure of the Bacillus Subtilis Enzyme at 1.9A Resolution
Authors: Vincent, F. / Charnock, S.J. / Verschueren, K.H.G. / Turkenburg, J.P. / Scott, D.J. / Offen, W.A. / Roberts, S. / Pell, G. / Gilbert, H.J. / Davies, G.J. / Brannigan, J.A.
History
DepositionFeb 20, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CEPHALOSPORIN C DEACETYLASE
B: CEPHALOSPORIN C DEACETYLASE
C: CEPHALOSPORIN C DEACETYLASE
D: CEPHALOSPORIN C DEACETYLASE
E: CEPHALOSPORIN C DEACETYLASE
F: CEPHALOSPORIN C DEACETYLASE
G: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,50518
Polymers287,1738
Non-polymers33210
Water37,0212055
1
A: CEPHALOSPORIN C DEACETYLASE
B: CEPHALOSPORIN C DEACETYLASE
hetero molecules

A: CEPHALOSPORIN C DEACETYLASE
B: CEPHALOSPORIN C DEACETYLASE
hetero molecules

A: CEPHALOSPORIN C DEACETYLASE
B: CEPHALOSPORIN C DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,73818
Polymers215,3796
Non-polymers35912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2
C: CEPHALOSPORIN C DEACETYLASE
D: CEPHALOSPORIN C DEACETYLASE
E: CEPHALOSPORIN C DEACETYLASE
F: CEPHALOSPORIN C DEACETYLASE
G: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,59212
Polymers215,3796
Non-polymers2136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)315.215, 315.215, 68.483
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.992, 0.127, 0.008), (0.127, -0.992, -0.003), (0.007, 0.004, -1)-10.29182, 161.16939, -1.11268
2given(-0.573, 0.816, -0.075), (-0.816, -0.559, 0.149), (0.08, 0.146, 0.986)0.98422, 2.34728, -0.01626
3given(-0.467, -0.881, 0.074), (-0.879, 0.453, -0.151), (0.1, -0.135, -0.986)2.42255, 1.48908, 0.13497
4given(-0.52953, 0.84474, 0.07755), (0.83168, 0.53499, -0.14864), (-0.16705, -0.01421, -0.98585)84.68312, -134.53432, 51.24715
5given(-0.41962, -0.90451, -0.07605), (0.89155, -0.42644, 0.15259), (-0.17045, -0.00377, 0.98536)226.47522, -56.56386, 50.60589
6given(0.99328, 0.09095, -0.07163), (-0.07902, 0.98481, 0.1546), (0.08461, -0.1479, 0.98538)-86.64191, -32.08704, 23.30945
7given(0.99586, 0.03973, 0.08172), (0.05176, -0.9872, -0.15086), (0.07468, 0.15446, -0.98517)-82.40652, 126.90166, -2.06212

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Components

#1: Protein
CEPHALOSPORIN C DEACETYLASE / MULTI-FUNCTIONAL ESTERASE / CAH


Mass: 35896.566 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P94388, cephalosporin-C deacetylase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2055 / 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: 2.3 Å3/Da / Density % sol: 45.5 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal
*PLUS
Density % sol: 46 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
230 %(v/v)MPD1reservoir
30.1 M1reservoirMgCl2
40.1 MMOPS1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786, 0.9786, 0.9184, 0.908
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.91841
30.9081
ReflectionResolution: 1.9→100 Å / Num. obs: 199895 / % possible obs: 99.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.9
Reflection shellHighest resolution: 1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4.4 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / % possible obs: 98.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→100 Å / SU B: 3.025 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.18611 10036 5 %RANDOM
Rwork0.15215 ---
obs0.15387 189201 99.67 %-
Displacement parametersBiso mean: 9.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20200 0 10 2055 22265
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / Rfactor Rfree: 0.186 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.011
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.32

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