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- PDB-5e9a: Crystal structure analysis of the cold-adamped beta-galactosidase... -

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Basic information

Entry
Database: PDB / ID: 5e9a
TitleCrystal structure analysis of the cold-adamped beta-galactosidase from Rahnella sp. R3
ComponentsBeta-galactosidase
KeywordsHYDROLASE / galactosidase / TIM barrel / lactose
Function / homology
Function and homology information


galactose metabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / metal ion binding
Similarity search - Function
Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II ...Beta-galactosidase C-terminal / Beta-galactosidase C-terminal domain / Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Beta-galactosidase
Similarity search - Component
Biological speciesRahnella sp. R3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.561 Å
AuthorsZhang, Y.Z. / Fan, Y.T.
CitationJournal: Protein Expr.Purif. / Year: 2015
Title: Cloning, expression and structural stability of a cold-adapted beta-galactosidase from Rahnella sp. R3.
Authors: Fan, Y. / Hua, X. / Zhang, Y. / Feng, Y. / Shen, Q. / Dong, J. / Zhao, W. / Zhang, W. / Jin, Z. / Yang, R.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / pdbx_struct_oper_list / struct
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
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: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,45318
Polymers481,7066
Non-polymers74712
Water7,710428
1
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,2269
Polymers240,8533
Non-polymers3736
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-74 kcal/mol
Surface area63950 Å2
MethodPISA
2
D: Beta-galactosidase
E: Beta-galactosidase
F: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,2269
Polymers240,8533
Non-polymers3736
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-76 kcal/mol
Surface area64020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.426, 106.831, 164.244
Angle α, β, γ (deg.)90.000, 109.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galactosidase / Beta-gal


Mass: 80284.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rahnella sp. R3 (bacteria) / Plasmid: pCold1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4U8I5, beta-galactosidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl, 30%(w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 18, 2014
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.561→138.448 Å / Num. all: 151929 / Num. obs: 151929 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rpim(I) all: 0.085 / Rrim(I) all: 0.163 / Rsym value: 0.116 / Net I/av σ(I): 6.434 / Net I/σ(I): 8.6 / Num. measured all: 535514
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.56-2.73.20.4851.669030217170.3490.4852.496.8
2.7-2.863.30.381268965206080.2710.381397.4
2.86-3.063.50.2682.968770196500.190.2684.198.3
3.06-3.313.60.1834.266735184600.1290.183699.5
3.31-3.623.70.126.462502170840.0850.12999.7
3.62-4.053.70.0868.856396153750.0610.08612.299.2
4.05-4.683.60.06510.949388135650.0470.06515.398.9
4.68-5.733.70.05812.142201114780.0410.05816.399.1
5.73-8.13.70.0514.13345390000.0350.0517.299.6
8.1-138.4483.60.03319.71807449920.0230.03322.398.5

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0131refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.561→138.448 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 12.614 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.7 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 2020 1.3 %RANDOM
Rwork0.1993 ---
obs0.2 149793 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.62 Å2 / Biso mean: 32.339 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å2-0.13 Å2
2---3.64 Å2-0 Å2
3---1.44 Å2
Refinement stepCycle: final / Resolution: 2.561→138.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32507 0 30 428 32965
Biso mean--38.23 21.14 -
Num. residues----4099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01933471
X-RAY DIFFRACTIONr_bond_other_d0.0030.0230649
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.92845541
X-RAY DIFFRACTIONr_angle_other_deg1.007370275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05154096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77323.5921662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.361155191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.79815230
X-RAY DIFFRACTIONr_chiral_restr0.0840.24760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02138696
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028364
X-RAY DIFFRACTIONr_mcbond_it1.8563.11416399
X-RAY DIFFRACTIONr_mcbond_other1.8553.11316392
X-RAY DIFFRACTIONr_mcangle_it2.9124.66620480
LS refinement shellResolution: 2.561→2.627 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 101 -
Rwork0.289 10822 -
all-10923 -
obs--96.38 %

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