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- PDB-5c3m: Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geob... -

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Basic information

Entry
Database: PDB / ID: 5c3m
TitleCrystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus
ComponentsPutative 6-phospho-beta-glucosidase
KeywordsHYDROLASE / Glycoside Hydrolase / Manganese / 6-phospho-glucosidase
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Glycoside hydrolase, family 4, conserved site / Glycosyl hydrolases family 4 signature. / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Putative 6-phospho-beta-glucosidase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.059 Å
AuthorsCohen, T. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
CitationJournal: To Be Published
Title: Crystal structure of Gan4C, a GH4 6-phospho-glucosidase from Geobacillus stearothermophilus
Authors: Cohen, T. / Lansky, S. / Zehavi, A. / Shoham, Y. / Shoham, G.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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: Putative 6-phospho-beta-glucosidase
B: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water1,63991
1
A: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
hetero molecules

A: Putative 6-phospho-beta-glucosidase
C: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9320 Å2
ΔGint-58 kcal/mol
Surface area59720 Å2
MethodPISA
2
B: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules

B: Putative 6-phospho-beta-glucosidase
D: Putative 6-phospho-beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5128
Polymers197,2924
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area9510 Å2
ΔGint-63 kcal/mol
Surface area58990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.324, 83.198, 151.372
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative 6-phospho-beta-glucosidase


Mass: 49322.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: gan4C / Production host: Escherichia coli (E. coli) / References: UniProt: W8R9V4, 6-phospho-beta-glucosidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 16% PEG 8K, 0.1M CHES buffer pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 39747 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 3.06→3.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S6Y

1s6y


Resolution: 3.059→46.603 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3061 1964 4.94 %
Rwork0.2295 --
obs0.2334 39747 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.059→46.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12399 0 4 91 12494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112639
X-RAY DIFFRACTIONf_angle_d1.24917187
X-RAY DIFFRACTIONf_dihedral_angle_d16.0474616
X-RAY DIFFRACTIONf_chiral_restr0.0561991
X-RAY DIFFRACTIONf_plane_restr0.0082237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.059-3.13540.46461380.3312434X-RAY DIFFRACTION91
3.1354-3.22020.34171560.29982648X-RAY DIFFRACTION97
3.2202-3.31490.38651370.28062692X-RAY DIFFRACTION99
3.3149-3.42190.3861130.27682683X-RAY DIFFRACTION100
3.4219-3.54410.36811480.27272699X-RAY DIFFRACTION100
3.5441-3.6860.3741450.26842718X-RAY DIFFRACTION100
3.686-3.85370.37971310.24312727X-RAY DIFFRACTION100
3.8537-4.05670.30861300.23772717X-RAY DIFFRACTION100
4.0567-4.31070.28151370.22142716X-RAY DIFFRACTION100
4.3107-4.64330.28961450.19522747X-RAY DIFFRACTION100
4.6433-5.110.2691540.19572708X-RAY DIFFRACTION100
5.11-5.84830.29871440.21662730X-RAY DIFFRACTION100
5.8483-7.36350.29281400.22162755X-RAY DIFFRACTION100
7.3635-46.60810.2151460.18532809X-RAY DIFFRACTION99

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