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- PDB-5jib: Crystal structure of the Thermotoga maritima acetyl esterase (TM0... -

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Basic information

Entry
Database: PDB / ID: 5jib
TitleCrystal structure of the Thermotoga maritima acetyl esterase (TM0077) complex with a substrate analog
ComponentsCephalosporin-C deacetylase
KeywordsHYDROLASE / CARBOHYDRATE METABOLISM / CEPHALOSPORIN DEACETYLASE / ROSSMANN 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
[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid / Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsManoj, N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology, Govt. of IndiaBT/PR13805/PID/06/550/2010 India
Citation
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.
#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.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)233,12512
Polymers231,9786
Non-polymers1,1476
Water18,7181039
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17740 Å2
ΔGint-119 kcal/mol
Surface area60300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.810, 115.780, 103.200
Angle α, β, γ (deg.)90.000, 109.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Cephalosporin-C deacetylase / / Acetylxylan esterase


Mass: 38662.922 Da / Num. of mol.: 6
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-OIA / [(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]acetic acid


Mass: 191.183 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H9NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 43.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M ammonium sulfate, 0.1 M 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: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→45.97 Å / Num. obs: 156655 / % possible obs: 94.3 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Rrim(I) all: 0.077 / Net I/σ(I): 19 / Num. measured all: 1178812 / Scaling rejects: 323
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 5.1 / % possible all: 70.7

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Processing

Software
NameVersionClassification
Aimless0.1.30data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FDF

5fdf


Resolution: 1.86→45.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.508 / SU ML: 0.076 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 7863 5 %RANDOM
Rwork0.1548 ---
obs0.1566 148760 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.16 Å2 / Biso mean: 19.604 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.23 Å2
2--0.3 Å2-0 Å2
3----0.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: final / Resolution: 1.86→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15120 0 84 1039 16243
Biso mean--32.14 26.6 -
Num. residues----1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915686
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214419
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.95521339
X-RAY DIFFRACTIONr_angle_other_deg1.113.00133108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52551908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65422.846738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.899152291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.85115105
X-RAY DIFFRACTIONr_chiral_restr0.1170.22208
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02117939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023898
X-RAY DIFFRACTIONr_mcbond_it1.7871.7717656
X-RAY DIFFRACTIONr_mcbond_other1.7841.777655
X-RAY DIFFRACTIONr_mcangle_it2.5572.6439553
LS refinement shellResolution: 1.863→1.912 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 516 -
Rwork0.184 10040 -
all-10556 -
obs--86.39 %

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