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- PDB-1odt: cephalosporin C deacetylase mutated, in complex with acetate -

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Basic information

Entry
Database: PDB / ID: 1odt
Titlecephalosporin C deacetylase mutated, in complex with acetate
ComponentsCEPHALOSPORIN C DEACETYLASE
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE / ACETYLXYLAN / CARBOHYDRATE ESTERASE / CEPHALOSPORIN
Function / homology
Function and homology information


cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / 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
ACETATE ION / Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7834
Polymers71,6652
Non-polymers1182
Water10,142563
1
C: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules

C: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules

C: CEPHALOSPORIN C DEACETYLASE
H: CEPHALOSPORIN C DEACETYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,34912
Polymers214,9956
Non-polymers3546
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)157.167, 157.170, 132.098
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-2053-

HOH

21H-2011-

HOH

31H-2061-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.991, 0.133), (0.133, -0.991, 0.003), (0.001, -0.003, -1)
Vector: -11.98389, 180.54744, 110.41402)

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Components

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


Mass: 35832.480 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH ACETATE / Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET26B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94388, cephalosporin-C deacetylase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN C, SER 181 TO ALA 181 ENGINEERED MUTATION IN CHAIN H, SER 181 TO ALA 181

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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: 2.2 Å3/Da / Density % sol: 43.1 %
Crystal growpH: 7.5
Details: 0.1M MOPS PH 6.5 0.2 M NA ACETATE 30% MPD , 0.1M MGCL2,
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %(v/v)MPD1reservoir
20.1 MTris-HCl1reservoirpH7.5
30.2 M1reservoirCaCl2
410 mMdithiothreitol1reservoir
50.2 Msodium acetate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→95 Å / Num. obs: 63610 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.9
Reflection shellHighest resolution: 1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.7 / % possible all: 95.9
Reflection
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 22 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Lowest resolution: 1.74 Å / % possible obs: 95.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ODS

1ods


Resolution: 1.7→95.35 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.004 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3376 5 %RANDOM
Rwork0.156 ---
obs0.158 63610 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.47 Å20 Å2
2---0.94 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5054 0 8 563 5625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215211
X-RAY DIFFRACTIONr_bond_other_d0.0020.024618
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9547074
X-RAY DIFFRACTIONr_angle_other_deg1.075310775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1310.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025800
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021078
X-RAY DIFFRACTIONr_nbd_refined0.2270.21109
X-RAY DIFFRACTIONr_nbd_other0.2460.25575
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.330.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7831.53164
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35225096
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.41332047
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7934.51978
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 241
Rwork0.224 4548
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)
10.3932-0.0330.08870.6111-0.09520.3823-0.00360.0493-0.0175-0.0398-0.0017-0.03730.01790.03770.00540.08920.00580.0150.115-0.00770.007226.33777.98543.412
20.4109-0.0219-0.05220.6824-0.10840.3956-0.0033-0.02360.02270.0347-0.0118-0.0481-0.03680.04920.0150.0837-0.0108-0.01220.0979-0.00730.015424.49106.89666.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 317
2X-RAY DIFFRACTION2H1 - 317
Refinement
*PLUS
Highest resolution: 1.69 Å / Lowest resolution: 22 Å / Rfactor Rwork: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.58

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