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- PDB-4pex: Structure of the E502A variant of sacteLam55A from Streptomyces s... -

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Basic information

Entry
Database: PDB / ID: 4pex
TitleStructure of the E502A variant of sacteLam55A from Streptomyces sp. SirexAA-E in complex with glucose
ComponentsPutative secreted proteinSecretory protein
KeywordsHYDROLASE / exo-beta-1 / 3-glucanase / beta-1 / GH55 / glucose / secreted / biomass degradation
Function / homologyglucan 1,3-beta-glucosidase / glucan exo-1,3-beta-glucosidase activity / glucan catabolic process / Pectin lyase fold / extracellular region / beta-D-glucopyranose / Exo-beta-1,3-glucanase
Function and homology information
Biological speciesStreptomyces sp. SirexAA-E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsBianchetti, C.M. / Takasuka, T.E. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Active site and laminarin binding in glycoside hydrolase family 55.
Authors: Bianchetti, C.M. / Takasuka, T.E. / Deutsch, S. / Udell, H.S. / Yik, E.J. / Bergeman, L.F. / Fox, B.G.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / struct_ref / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ref.pdbx_seq_one_letter_code
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 secreted protein
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6368
Polymers120,1452
Non-polymers4906
Water15,655869
1
A: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1973
Polymers60,0731
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4395
Polymers60,0731
Non-polymers3664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.939, 100.055, 99.556
Angle α, β, γ (deg.)90.000, 92.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 60072.637 Da / Num. of mol.: 2 / Fragment: UNP residues 46-605 / Mutation: E502A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SirexAA-E (bacteria) / Gene: SACTE_4363 / Plasmid: PVP67K / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2NFJ9
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% ...Details: Protein Solution (20 mg/ml protein, 0.05 M NaCl, and 0.010 M MOPS pH 7) mixed in a 1:1 ratio with the Well Solution (20% PEG 3350, 125mM NaCH02, and 100mM BTP pH 6.5). Cryoprotected with 20% PEG 3350, 125mM NaCH02, 75mM Glucose, 100mM BTP pH 6.5 and 15% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 123726 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 15.89 Å2 / Rmerge(I) obs: 0.082 / Χ2: 0.869 / Net I/av σ(I): 13.488 / Net I/σ(I): 7.2 / Num. measured all: 462173
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.66-1.693.50.54661910.589100
1.69-1.723.60.48961420.632100
1.72-1.753.60.43661440.667100
1.75-1.793.60.37362190.714100
1.79-1.833.60.33761230.777100
1.83-1.873.60.29161880.823100
1.87-1.923.60.24262160.921100
1.92-1.973.60.21561250.985100
1.97-2.033.60.18962011.041100
2.03-2.093.70.16661491.08100
2.09-2.173.70.14661971.078100
2.17-2.253.70.13461731.118100
2.25-2.363.80.12261861.116100
2.36-2.483.80.11162001.097100
2.48-2.633.90.10661821.159100
2.63-2.843.90.08962251.094100
2.84-3.1240.06962090.886100
3.12-3.5840.05162100.69299.8
3.58-4.540.03662110.48199.6
4.5-503.90.03362350.41598.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEW

4pew


Resolution: 1.75→24.265 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 5253 5.01 %Random selection
Rwork0.1407 99618 --
obs0.1423 104871 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.58 Å2 / Biso mean: 17.9898 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 1.75→24.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8339 0 32 869 9240
Biso mean--18.41 30.4 -
Num. residues----1099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158763
X-RAY DIFFRACTIONf_angle_d1.45412004
X-RAY DIFFRACTIONf_chiral_restr0.0881283
X-RAY DIFFRACTIONf_plane_restr0.0081618
X-RAY DIFFRACTIONf_dihedral_angle_d13.2923083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.76990.24011660.17842891305787
1.7699-1.79070.2011590.16753061322091
1.7907-1.81250.21711680.16013090325893
1.8125-1.83550.19931550.15343230338596
1.8355-1.85960.19871800.14953358353899
1.8596-1.88510.18211700.151232873457100
1.8851-1.9120.19191950.139433433538100
1.912-1.94050.18151660.140133443510100
1.9405-1.97080.17981750.140733453520100
1.9708-2.00310.17721770.138133703547100
2.0031-2.03760.18881880.137933133501100
2.0376-2.07470.18231680.136134323600100
2.0747-2.11460.17571730.136533203493100
2.1146-2.15770.17951750.135533653540100
2.1577-2.20460.17291810.132233303511100
2.2046-2.25580.18411800.144433703550100
2.2558-2.31220.19411600.139733793539100
2.3122-2.37470.191830.142133573540100
2.3747-2.44450.19171750.141533623537100
2.4445-2.52330.16251740.142433593533100
2.5233-2.61340.1731900.146733513541100
2.6134-2.71790.17351700.138233903560100
2.7179-2.84140.17881770.139333563533100
2.8414-2.9910.16291740.135233913565100
2.991-3.1780.17511770.140133723549100
3.178-3.42270.13271800.129933533533100
3.4227-3.7660.16891730.127833513524100
3.766-4.30830.13231780.13333843562100
4.3083-5.41810.14911800.13123347352798
5.4181-24.26720.19751860.17693417360399

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