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- PDB-5gma: Crystal structure of the P228A variant of Thermotoga maritima ace... -

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Basic information

Entry
Database: PDB / ID: 5gma
TitleCrystal structure of the P228A variant of Thermotoga maritima acetyl esterase
ComponentsCephalosporin-C deacetylase
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / CEPHALOSPORIN DEACETYLASE / ROSSMAN FOLD
Function / homology
Function and homology information


xylan metabolic process / cephalosporin C metabolic process / cephalosporin-C deacetylase / cephalosporin-C deacetylase activity / polysaccharide metabolic process / acetylxylan esterase / acetylxylan esterase activity / carboxylic ester hydrolase activity / cellulose catabolic process / calcium ion binding / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsManoj, N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of BiotechnologyBT/PR13805/PID/06/550/2010 India
Citation
Journal: Proteins / Year: 2017
Title: Structural role of a conserved active site cis proline in the Thermotoga maritima acetyl esterase from the carbohydrate esterase family 7
Authors: Singh, M.K. / Manoj, N.
#1: Journal: J. Struct. Biol. / Year: 2016
Title: An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability.
Authors: Singh, M.K. / Manoj, N.
#2: Journal: Biochem. Biophys. Res. Commun. / Year: 2016
Title: Crystal structure of Thermotoga maritima acetyl esterase complex with a substrate analog: Insights into the distinctive substrate specificity in the CE7 carbohydrate esterase family.
Authors: Singh, M.K. / Manoj, N.
History
DepositionJul 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,9989
Polymers231,8216
Non-polymers1773
Water13,637757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-146 kcal/mol
Surface area59990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.760, 115.690, 103.240
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cephalosporin-C deacetylase / Acetylxylan esterase


Mass: 38636.883 Da / Num. of mol.: 6 / Mutation: P228A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: axeA, TM_0077 / Plasmid: pMH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: Q9WXT2, cephalosporin-C deacetylase, acetylxylan esterase
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.1M Bis-Tris pH 6.5 and 30%(V/V) pentaerythritolethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 25, 2014
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50.14 Å / Num. obs: 115330 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 15.95 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
iMOSFLM7.1.1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FDF

5fdf


Resolution: 2.1→50.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.241 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21359 5781 5 %RANDOM
Rwork0.17611 ---
obs0.17799 109517 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20.17 Å2
2--0.65 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15307 0 12 757 16076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915829
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214578
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9521526
X-RAY DIFFRACTIONr_angle_other_deg0.956333456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35351944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10122.828746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.366152341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40815106
X-RAY DIFFRACTIONr_chiral_restr0.0840.22234
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02118153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023935
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1031.9867779
X-RAY DIFFRACTIONr_mcbond_other1.1011.9857775
X-RAY DIFFRACTIONr_mcangle_it1.8182.9719711
X-RAY DIFFRACTIONr_mcangle_other1.8182.9719712
X-RAY DIFFRACTIONr_scbond_it1.232.1098050
X-RAY DIFFRACTIONr_scbond_other1.232.1098051
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0363.11211813
X-RAY DIFFRACTIONr_long_range_B_refined3.60416.15218540
X-RAY DIFFRACTIONr_long_range_B_other3.60416.15318541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 418 -
Rwork0.24 8083 -
obs--99.87 %

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