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- PDB-9ms5: Crystal structure of an expansin (Ss_EXLX1) from Streptomyces sp. -

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Basic information

Entry
Database: PDB / ID: 9ms5
TitleCrystal structure of an expansin (Ss_EXLX1) from Streptomyces sp.
ComponentsPeptidoglycan-binding domain-containing protein, expansin
KeywordsSUGAR BINDING PROTEIN / bacterial expansin / carbohydrate-binding / cellulose-loosening
Function / homology: / : / RlpA-like protein, double-psi beta-barrel domain / Lytic transglycolase / Expansin, cellulose-binding-like domain superfamily / RlpA-like domain superfamily / Peptidoglycan-binding domain-containing protein, expansin
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSmith, C.A. / Buchko, G.W. / Momeni, M.H. / Master, E.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Insights into the action of phylogenetically diverse microbial expansins
Authors: Buchko, G.W. / Smith, C.A. / Momeni, M.H. / Master, E.R.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan-binding domain-containing protein, expansin
B: Peptidoglycan-binding domain-containing protein, expansin
C: Peptidoglycan-binding domain-containing protein, expansin
D: Peptidoglycan-binding domain-containing protein, expansin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,58513
Polymers87,4384
Non-polymers1,1479
Water12,755708
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.396, 101.634, 116.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Peptidoglycan-binding domain-containing protein, expansin / Ss_EXLX1


Mass: 21859.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: SAMN04487980_1008232 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1I4V6A4
#2: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris: HCl, pH 6.5 , 20 % (w/v) PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→76.7 Å / Num. obs: 140101 / % possible obs: 97 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rpim(I) all: 0.071 / Rrim(I) all: 0.141 / Net I/σ(I): 10.5
Reflection shellResolution: 1.45→1.487 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7005 / CC1/2: 0.672 / Rpim(I) all: 0.957

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→50.66 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 6999 5 %
Rwork0.1671 --
obs0.1687 140016 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→50.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 76 708 6912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056402
X-RAY DIFFRACTIONf_angle_d0.7858733
X-RAY DIFFRACTIONf_dihedral_angle_d16.7762352
X-RAY DIFFRACTIONf_chiral_restr0.083949
X-RAY DIFFRACTIONf_plane_restr0.0091159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.31651290.28052503X-RAY DIFFRACTION55
1.47-1.480.2481560.20673432X-RAY DIFFRACTION75
1.48-1.50.22022140.20444077X-RAY DIFFRACTION91
1.5-1.520.2352510.20094395X-RAY DIFFRACTION97
1.52-1.540.23632170.20014489X-RAY DIFFRACTION99
1.54-1.560.25582390.18374504X-RAY DIFFRACTION99
1.56-1.580.21592160.17624508X-RAY DIFFRACTION100
1.58-1.610.22492290.17034526X-RAY DIFFRACTION100
1.61-1.630.21412110.16574559X-RAY DIFFRACTION100
1.63-1.660.20162700.15714496X-RAY DIFFRACTION100
1.66-1.690.21472410.16094505X-RAY DIFFRACTION100
1.69-1.720.20592210.16134565X-RAY DIFFRACTION100
1.72-1.750.20742440.15874506X-RAY DIFFRACTION100
1.75-1.790.22112570.15594475X-RAY DIFFRACTION99
1.79-1.830.18052580.15174528X-RAY DIFFRACTION100
1.83-1.870.19412550.15274508X-RAY DIFFRACTION100
1.87-1.920.20612550.15134576X-RAY DIFFRACTION100
1.92-1.970.19312590.14384524X-RAY DIFFRACTION100
1.97-2.030.1662390.14684550X-RAY DIFFRACTION100
2.03-2.090.20562440.15044549X-RAY DIFFRACTION100
2.09-2.170.18292190.14944583X-RAY DIFFRACTION100
2.17-2.250.18472510.15224569X-RAY DIFFRACTION100
2.25-2.360.19122250.16054593X-RAY DIFFRACTION100
2.36-2.480.19062270.1654565X-RAY DIFFRACTION100
2.48-2.640.20862300.17184575X-RAY DIFFRACTION99
2.64-2.840.1992830.1734575X-RAY DIFFRACTION100
2.84-3.120.21352440.18124611X-RAY DIFFRACTION100
3.12-3.580.18362340.1744682X-RAY DIFFRACTION100
3.58-4.510.18622380.16384706X-RAY DIFFRACTION100
4.51-50.660.18322430.17734783X-RAY DIFFRACTION98

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