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- PDB-8wae: Crystal structure of a novel porphyran-binding carbohydrate bindi... -

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Basic information

Entry
Database: PDB / ID: 8wae
TitleCrystal structure of a novel porphyran-binding carbohydrate binding module
ComponentsBeta-agarase
KeywordsSUGAR BINDING PROTEIN / A novel porphyran-binding carbohydrate binding module
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Porphyranase catalytic subdomain 1 / Beta-porphyranase A, C-terminal / beta porphyranase A C-terminal / Porphyranase beta-sandwich domain 1 / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. ...Porphyranase catalytic subdomain 1 / Beta-porphyranase A, C-terminal / beta porphyranase A C-terminal / Porphyranase beta-sandwich domain 1 / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesFlammeovirga sp. OC4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMei, X.W. / Chang, Y.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of a novel porphyran-binding carbohydrate binding module
Authors: Mei, X.W. / Chang, Y.G.
History
DepositionSep 7, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-agarase
B: Beta-agarase


Theoretical massNumber of molelcules
Total (without water)25,0322
Polymers25,0322
Non-polymers00
Water7,548419
1
A: Beta-agarase


Theoretical massNumber of molelcules
Total (without water)12,5161
Polymers12,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-agarase


Theoretical massNumber of molelcules
Total (without water)12,5161
Polymers12,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.079, 49.421, 160.895
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 Beta-agarase


Mass: 12515.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flammeovirga sp. OC4 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D5CS34
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.75→49.42 Å / Num. obs: 21203 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Χ2: 1.03 / Net I/σ(I): 25.8 / Num. measured all: 130924
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.095 / Num. measured all: 5930 / Num. unique obs: 1150 / CC1/2: 0.992 / Rpim(I) all: 0.046 / Rrim(I) all: 0.106 / Χ2: 0.95 / Net I/σ(I) obs: 13.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→24.78 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 2000 9.47 %
Rwork0.1571 --
obs0.1618 21115 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 0 419 1992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.868
X-RAY DIFFRACTIONf_dihedral_angle_d6.123250
X-RAY DIFFRACTIONf_chiral_restr0.065295
X-RAY DIFFRACTIONf_plane_restr0.007315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.25221440.17251374X-RAY DIFFRACTION100
1.79-1.840.25161360.17391299X-RAY DIFFRACTION100
1.84-1.90.21691390.16541339X-RAY DIFFRACTION100
1.9-1.960.22571410.17031342X-RAY DIFFRACTION100
1.96-2.030.21591370.15581314X-RAY DIFFRACTION100
2.03-2.110.20341430.15371356X-RAY DIFFRACTION100
2.11-2.20.19981390.15021338X-RAY DIFFRACTION100
2.2-2.320.23081420.16881356X-RAY DIFFRACTION99
2.32-2.470.2421420.1621356X-RAY DIFFRACTION100
2.47-2.660.20021410.16641356X-RAY DIFFRACTION100
2.66-2.920.1911450.15781382X-RAY DIFFRACTION100
2.92-3.350.19451450.14981383X-RAY DIFFRACTION100
3.35-4.210.19391490.13951423X-RAY DIFFRACTION100
4.21-24.780.18261570.15691497X-RAY DIFFRACTION100

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