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- PDB-7jjn: Eubacterium rectale Amy13B (EUR_01860) -

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Basic information

Entry
Database: PDB / ID: 7jjn
TitleEubacterium rectale Amy13B (EUR_01860)
ComponentsGlycosidases
KeywordsHYDROLASE / maltogenic amylase / GH13_16 / GH13 / amylase
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process
Similarity search - Function
Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-maltotriose / Glycosidases
Similarity search - Component
Biological species[Eubacterium] rectale DSM 17629 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsKoropatkin, N.M. / Cockburn, D.W. / Cerqueira, F.M.
CitationJournal: Amylase / Year: 2020
Title: The structures of the GH13_36 amylases from Eubacterium rectale and Ruminococcus bromii reveal subsite architectures that favor maltose production
Authors: Cockburn, D.W. / Cerqueira, F.M. / Bahr, C.M.E. / Koropatkin, N.M.
History
DepositionJul 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Glycosidases
B: Glycosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,37412
Polymers118,7852
Non-polymers1,58910
Water9,782543
1
A: Glycosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1876
Polymers59,3921
Non-polymers7955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosidases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1876
Polymers59,3921
Non-polymers7955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.180, 82.760, 85.860
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glycosidases


Mass: 59392.441 Da / Num. of mol.: 2 / Mutation: D265A K543A K544A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] rectale DSM 17629 (bacteria)
Gene: EUR_01860 / Plasmid: pETite Nhis / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II / References: UniProt: D6E1Y4, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 551 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.17M Am Sulfate, 25.5% PEG 4000, 15% glycerol (JCSG+ screen, Molecular Dimensions)
Temp details: room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen vapor / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→38.07 Å / Num. obs: 55448 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.16 / Net I/σ(I): 9.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.84 / Num. unique obs: 5536 / CC1/2: 0.77 / CC star: 0.93 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZA

1wza


Resolution: 2.25→38.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.678 / SU ML: 0.145 / SU R Cruickshank DPI: 0.2637 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 2783 5 %RANDOM
Rwork0.1621 ---
obs0.1639 52665 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.48 Å2 / Biso mean: 34.396 Å2 / Biso min: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20.86 Å2
2--0.63 Å20 Å2
3----0.22 Å2
Refinement stepCycle: final / Resolution: 2.25→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8144 0 100 543 8787
Biso mean--41.79 39.05 -
Num. residues----1023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0148431
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177139
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.67211437
X-RAY DIFFRACTIONr_angle_other_deg0.8391.66116771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40251019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07724.644463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.481151358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.891526
X-RAY DIFFRACTIONr_chiral_restr0.0560.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021628
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 239 -
Rwork0.251 3835 -
all-4074 -
obs--99.51 %
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)
11.7259-0.2576-0.53430.52330.04140.81490.01170.023-0.0143-0.0432-0.0314-0.0339-0.04970.00440.01970.0332-0.03070.00590.0462-0.00040.00553.453738.833611.073
21.3692-0.4218-0.54960.89010.40161.34920.00250.10090.0321-0.02240.004-0.0505-0.13080.0973-0.00650.0171-0.00480.00630.08020.04030.028528.04854.581225.1626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 701
2X-RAY DIFFRACTION2B55 - 701

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