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- PDB-7lst: Ruminococcus bromii Amy12-D392A with 63-a-D-glucosyl-maltotriosyl... -

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Basic information

Entry
Database: PDB / ID: 7lst
TitleRuminococcus bromii Amy12-D392A with 63-a-D-glucosyl-maltotriosyl-maltotriose
ComponentsPullulanase
KeywordsHYDROLASE / GH13 / pullulanase / CBM48 / complex
Function / homology
Function and homology information


pullulanase / pullulanase activity / cellulose catabolic process / extracellular region / metal ion binding
Similarity search - Function
MucBP domain / MucBP domain / Starch-binding module 26 / Starch-binding module 26 / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Dockerin domain / Dockerin domain profile. / Dockerin type I domain ...MucBP domain / MucBP domain / Starch-binding module 26 / Starch-binding module 26 / Pullulanase, type I / Glycoside hydrolase, family 13, N-terminal / Carbohydrate-binding module 48 (Isoamylase N-terminal domain) / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
beta-maltotriose / ACETATE ION / pullulanase
Similarity search - Component
Biological speciesRuminococcus bromii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsKoropatkin, N.M. / Cockburn, D.W. / Brown, H.A. / Kibler, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF) United States
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structure and substrate recognition by the Ruminococcus bromii amylosome pullulanases.
Authors: Cockburn, D.W. / Kibler, R. / Brown, H.A. / Duvall, R. / Morais, S. / Bayer, E. / Koropatkin, N.M.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 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: Pullulanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,51123
Polymers87,4581
Non-polymers2,05322
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.981, 99.107, 167.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Pullulanase


Mass: 87458.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii (bacteria) / Gene: pulA_2, RBL236_00821 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A2N0UU23, pullulanase
#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.: 1
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, 617 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8.75 - 8.9 mg/ml of protein and 10 mM 63-a-D-glucosyl-maltotriosyl-maltotriose via hanging drop against a well solution containing 16% PEG 3350, 4% glycerol, 0.3 ammonium acetate, and 0.1 M Bis-Tris pH 6.5.

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Data collection

DiffractionMean temperature: 120 K / Ambient temp details: crogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2016
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→85.3 Å / Num. obs: 49996 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.99 / Net I/σ(I): 5.9
Reflection shellResolution: 2.05→2.12 Å / Num. unique obs: 4926 / CC1/2: 0.64

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LSA

7lsa


Resolution: 2.05→85.26 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 14.488 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2487 5 %RANDOM
Rwork0.1799 ---
obs0.1824 47508 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.32 Å2 / Biso mean: 23.062 Å2 / Biso min: 10.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---1.12 Å20 Å2
3---1.17 Å2
Refinement stepCycle: final / Resolution: 2.05→85.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5878 0 134 596 6608
Biso mean--33.33 27.15 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0146119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185253
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.6758292
X-RAY DIFFRACTIONr_angle_other_deg0.7531.6812287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8145762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39624.075292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99215954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3641519
X-RAY DIFFRACTIONr_chiral_restr0.0390.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_rigid_bond_restr0.32311372
X-RAY DIFFRACTIONr_sphericity_free25.8585336
X-RAY DIFFRACTIONr_sphericity_bonded8.971511525
LS refinement shellResolution: 2.05→2.102 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.347 180 -
Rwork0.303 3341 -
obs--97.16 %
Refinement TLS params.Method: refined / Origin x: 62.3055 Å / Origin y: 101.3478 Å / Origin z: 188.202 Å
111213212223313233
T0.0502 Å20.0025 Å20.0045 Å2-0.1536 Å20.0082 Å2--0.0136 Å2
L0.4043 °2-0.1383 °2-0.1119 °2-0.4318 °20.1549 °2--0.9997 °2
S0.0397 Å °0.0614 Å °0.0735 Å °-0.1323 Å °-0.0193 Å °-0.0203 Å °-0.0565 Å °0.0185 Å °-0.0203 Å °

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