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- PDB-5fdf: Crystal structure of the monoclinic form of Thermotoga maritima A... -

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Basic information

Entry
Database: PDB / ID: 5fdf
TitleCrystal structure of the monoclinic form of Thermotoga maritima Acetyl Esterase TM0077 (apo structure) at 1.76 Angstrom resolution
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
ACETATE ION / Cephalosporin-C deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsManoj, N. / Singh, M.K.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology, Government of IndiaBT/PR13805/PID/06/550/2010 India
CitationJournal: 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
DepositionDec 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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)232,0728
Polymers231,9786
Non-polymers942
Water26,7881487
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18240 Å2
ΔGint-131 kcal/mol
Surface area60900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.760, 116.200, 103.290
Angle α, β, γ (deg.)90.000, 109.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38662.922 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: cytoplasm / Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: axeA, TM_0077 / Plasmid: pMH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: Q9WXT2, cephalosporin-C deacetylase, acetylxylan esterase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1487 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05 M Ammonium sulfate, 0.05 M BIS-TRIS pH 6.5 and 30% (V/V) Pentaerythritol ethoxylate (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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→39.96 Å / Num. obs: 194397 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.047 / Net I/σ(I): 11.5 / Num. measured all: 1297873 / Scaling rejects: 291
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.76-1.796.30.981.95949494090.5250.41496.6
9.64-39.966.70.04731832612440.9970.0298.4

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
AMoREphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLQ

1vlq


Resolution: 1.76→39.96 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.576 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / SU Rfree Cruickshank DPI: 0.1058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 9696 5 %RANDOM
Rwork0.1597 ---
obs0.1615 184681 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 69.28 Å2 / Biso mean: 21.9 Å2 / Biso min: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.04 Å2
2--0.28 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.76→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15211 0 5 1487 16703
Biso mean--34.32 32.3 -
Num. residues----1918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915778
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214511
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.94921467
X-RAY DIFFRACTIONr_angle_other_deg1.058333346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46151930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4722.953762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.795152346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.36815107
X-RAY DIFFRACTIONr_chiral_restr0.120.22216
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118084
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023927
X-RAY DIFFRACTIONr_mcbond_it1.8431.9797697
X-RAY DIFFRACTIONr_mcbond_other1.8371.9787695
X-RAY DIFFRACTIONr_mcangle_it2.5592.9579616
LS refinement shellHighest resolution: 1.76 Å

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