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- PDB-9m0b: Crystal structure of alpha-agarase AGA from Catenovulum maritimum -

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Basic information

Entry
Database: PDB / ID: 9m0b
TitleCrystal structure of alpha-agarase AGA from Catenovulum maritimum
ComponentsAlpha-agarase
KeywordsHYDROLASE / Glycoside Hydrolase / Structural Genomics / PSI-Biology
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / calcium ion binding
Similarity search - Function
Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / Cellulose binding, type IV / Cellulose Binding Domain Type IV / PA14/GLEYA domain / PA14 domain profile. / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / DI(HYDROXYETHYL)ETHER / Alpha-agarase
Similarity search - Component
Biological speciesCatenovulum maritimum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsZhang, X.M. / Li, W.H. / Han, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32060039 China
CitationJournal: To Be Published
Title: Crystal structure of alpha-agarase AGA from Catenovulum maritimum
Authors: Zhang, X.M. / Li, W.H. / Han, X.D.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-agarase
B: Alpha-agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,17440
Polymers172,3542
Non-polymers2,82038
Water24,6271367
1
A: Alpha-agarase
hetero molecules

B: Alpha-agarase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,17440
Polymers172,3542
Non-polymers2,82038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6180 Å2
ΔGint-250 kcal/mol
Surface area58110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.242, 136.065, 109.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-agarase / Agarase AGA


Mass: 86176.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catenovulum maritimum (bacteria) / Gene: XM47_01860
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0J8H064

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Non-polymers , 9 types, 1405 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: Ammonium Sulfate, HEPES pH7.8, PEG8000

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Data collection

DiffractionMean temperature: 278 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979137 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Dec 21, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979137 Å / Relative weight: 1
ReflectionResolution: 1.64→109.17 Å / Num. obs: 234458 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.013 / Rrim(I) all: 0.048 / Net I/σ(I): 9
Reflection shellResolution: 1.64→1.76 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.047 / Mean I/σ(I) obs: 10.7 / Num. unique obs: 9791 / Rpim(I) all: 0.013 / Rrim(I) all: 0.049 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIXv1.2refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→109.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.559 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22012 11632 5 %RANDOM
Rwork0.1871 ---
obs0.18876 222367 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å20 Å2
2---0.57 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.64→109.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12198 0 162 1367 13727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01212750
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611283
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.78917380
X-RAY DIFFRACTIONr_angle_other_deg0.5941.73925933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20451567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.798557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.706101840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.21824
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2452.2886202
X-RAY DIFFRACTIONr_mcbond_other2.2452.2886202
X-RAY DIFFRACTIONr_mcangle_it3.2424.1047755
X-RAY DIFFRACTIONr_mcangle_other3.2424.1047756
X-RAY DIFFRACTIONr_scbond_it3.1112.6096548
X-RAY DIFFRACTIONr_scbond_other3.0242.5846509
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7064.5999554
X-RAY DIFFRACTIONr_long_range_B_refined6.56326.414951
X-RAY DIFFRACTIONr_long_range_B_other6.44724.9114599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.641→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 753 -
Rwork0.342 16221 -
obs--98.66 %

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