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- PDB-7jjt: Ruminococcus bromii amylase Amy5 (RBR_07800) -

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Basic information

Entry
Database: PDB / ID: 7jjt
TitleRuminococcus bromii amylase Amy5 (RBR_07800)
ComponentsAlpha-amylase
KeywordsHYDROLASE / amylase / GH13 / GH13_36 / glycoside hydrolase 13
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / cation binding / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process
Similarity search - Function
Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Alpha-amylase
Similarity search - Component
Biological speciesRuminococcus bromii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsCerqueira, F. / Koropatkin, N.
Funding support United States, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF) United States
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: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,01527
Polymers58,4861
Non-polymers1,52926
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.460, 98.460, 196.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1456-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase


Mass: 58486.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii (bacteria) / Gene: RBL236_00453 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 rosetta pLyss / References: UniProt: A0A2N0UXJ4, alpha-amylase

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Non-polymers , 5 types, 804 molecules

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


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.07 Å3/Da / Density % sol: 69.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.02M Zinc Chloride and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / 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: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.66→44.001 Å / Num. obs: 114177 / % possible obs: 99.9 % / Redundancy: 9.8 % / CC1/2: 0.997 / Net I/σ(I): 10.58
Reflection shellResolution: 1.66→1.719 Å / Num. unique obs: 11264 / CC1/2: 0.694

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WZA

1wza


Resolution: 1.66→44.001 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.181 5739 5.03 %
Rwork0.1602 108381 -
obs0.1612 114120 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.99 Å2 / Biso mean: 31.8256 Å2 / Biso min: 15.72 Å2
Refinement stepCycle: final / Resolution: 1.66→44.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 224 778 5038
Biso mean--51.24 41.36 -
Num. residues----513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.66-1.67890.30051730.30053580
1.6789-1.69860.29651920.29653576
1.6986-1.71930.28181820.28183547
1.7193-1.74110.3051700.25813554
1.7411-1.7640.25852010.25853563
1.764-1.78820.26541860.24663576
1.7882-1.81370.25391780.22823544
1.8137-1.84080.25821930.21943582
1.8408-1.86960.24551800.21493563
1.8696-1.90020.24491790.21593581
1.9002-1.9330.24112040.20223582
1.933-1.96810.21971790.19123584
1.9681-2.0060.21631890.19433576
2.006-2.04690.21331940.18713589
2.0469-2.09140.1841860.17233594
2.0914-2.14010.19552060.16823577
2.1401-2.19360.19121890.17063565
2.1936-2.25290.17211730.16083622
2.2529-2.31920.18871870.15473602
2.3192-2.39410.18242070.15583605
2.3941-2.47960.18151890.15083602
2.4796-2.57890.17111880.15573628
2.5789-2.69620.17122140.14843584
2.6962-2.83840.15682040.14593636
2.8384-3.01620.1781980.14713646
3.0162-3.2490.17861890.14963654
3.249-3.57580.17191960.14113675
3.5758-4.09290.14162010.13143718
4.0929-5.15530.13162030.11563740
5.1553-44.0010.18332090.16613936

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