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- PDB-1l7a: structural Genomics, crystal structure of Cephalosporin C deacetylase -

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Basic information

Entry
Database: PDB / ID: 1l7a
Titlestructural Genomics, crystal structure of Cephalosporin C deacetylase
ComponentsCephalosporin C deacetylase
KeywordsHYDROLASE / structural genomics / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsZhang, R. / Koroleva, O. / Collert, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of the Cephalosporin C deacetylase
Authors: Zhang, R. / Koroleva, O. / Collert, F. / Joachimiak, A.
History
DepositionMar 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)71,7852
Polymers71,7852
Non-polymers00
Water9,062503
1
A: Cephalosporin C deacetylase
B: Cephalosporin C deacetylase

A: Cephalosporin C deacetylase
B: Cephalosporin C deacetylase

A: Cephalosporin C deacetylase
B: Cephalosporin C deacetylase


Theoretical massNumber of molelcules
Total (without water)215,3566
Polymers215,3566
Non-polymers00
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
Unit cell
Length a, b, c (Å)156.446, 156.446, 131.748
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Cephalosporin C deacetylase


Mass: 35892.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: CAH / Plasmid: pmcsg7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P94388, cephalosporin-C deacetylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.9791, 0.9520
DetectorType: SBC-2 / Detector: CCD / Date: Feb 6, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.9521
ReflectionResolution: 1.5→50 Å / Num. all: 96880 / Num. obs: 96738 / % possible obs: 99.85 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 10.92 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 27.78
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.54 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.955 / Num. unique all: 12039 / % possible all: 99.6

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→47.73 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 276511.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections used in refinement include Friedel pairs. Therefore, the number of reflections for refinement is larger than the number collected.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 9185 5 %RANDOM
Rwork0.185 ---
all0.186 ---
obs0.186 185125 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5819 Å2 / ksol: 0.38572 e/Å3
Displacement parametersBiso mean: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.49 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.5→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 503 5577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d1.94
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.212 1429 4.9 %
Rwork0.21 27835 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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