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- PDB-4ce7: Crystal structure of a novel unsaturated beta-glucuronyl hydrolas... -

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Basic information

Entry
Database: PDB / ID: 4ce7
TitleCrystal structure of a novel unsaturated beta-glucuronyl hydrolase enzyme, belonging to family GH105, involved in ulvan degradation
ComponentsUNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE
KeywordsHYDROLASE / EXO-ENZYME / ULVAN DEGRADATION / FAMILY GH105 / MARINE POLYSACCHARIDE
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / carbohydrate metabolic process / hydrolase activity / plasma membrane
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / Unsaturated 3S-rhamnoglycuronyl hydrolase
Similarity search - Component
Biological speciesNONLABENS ULVANIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsNyvall Collen, P. / Jeudy, A. / Groisillier, A. / Coutinho, P.M. / Helbert, W. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A Novel Unsaturated Beta-Glucuronyl Hydrolase Involved in Ulvan Degradation Unveils the Versatility of Stereochemistry Requirements in Family Gh105.
Authors: Nyvall-Collen, P. / Jeudy, A. / Sassi, J. / Groisillier, A. / Czjzek, M. / Coutinho, P.M. / Helbert, W.
History
DepositionNov 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE
B: UNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE
C: UNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6727
Polymers129,4243
Non-polymers2484
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-13.4 kcal/mol
Surface area47740 Å2
MethodPQS
Unit cell
Length a, b, c (Å)92.978, 93.331, 156.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPROAA14 - 21022 - 218
21ASPASPPROPROBB14 - 21022 - 218
31ASPASPPROPROCC14 - 21022 - 218
12ARGARGVALVALAA219 - 325227 - 333
22ARGARGVALVALBB219 - 325227 - 333
32ARGARGVALVALCC219 - 325227 - 333
13VALVALMETMETAA325 - 361333 - 369
23VALVALMETMETBB325 - 361333 - 369
33VALVALMETMETCC325 - 361333 - 369

NCS oper:
IDCodeMatrixVector
1given(0.17892, 0.98254, -0.05106), (0.18243, 0.01787, 0.98306), (0.9668, -0.1852, -0.17605)-15.42627, 8.70605, 11.33162
2given(0.1892, 0.22046, 0.95687), (0.98087, 0.003, -0.19464), (-0.04578, 0.97539, -0.21567)-11.48146, 18.17165, -6.17053
3given(0.188767, 0.980944, -0.045991), (0.221133, 0.00317, 0.975239), (0.9568, -0.194263, -0.216321)-15.90984, 8.47821, 13.22033

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Components

#1: Protein UNSATURATED 3S-RHAMNOGLYCURONYL HYDROLASE / UNSATURATED BETA-GLUCURONYL HYDROLASE


Mass: 43141.184 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NONLABENS ULVANIVORANS (bacteria)
Description: ISOLATED AND AVALIABLE AT STATION BIOLOGIQUE DE ROSCOFF AND DEPOSITED AT GERMAN COLLECTION OF MICROORGANISMS (DSM)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: L7P9J4, unsaturated rhamnogalacturonyl hydrolase
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growpH: 8.5
Details: 100 MM TRIS BUFFER AT PH 8.5, 24 % (W/V) PEG MME 2000, 0.2 M POTASSIUM NITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→80.2 Å / Num. obs: 107955 / % possible obs: 99.1 % / Observed criterion σ(I): 0.1 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→45.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.503 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20685 5312 5 %RANDOM
Rwork0.16239 ---
obs0.16459 101396 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 16 742 9284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.028880
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.92312056
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03151050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94924.435469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.684151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1311539
X-RAY DIFFRACTIONr_chiral_restr0.1870.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216969
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 344 -
Rwork0.293 7089 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45740.00220.33220.7870.0620.61660.00990.00960.0027-0.0445-0.01410.0781-0.0547-0.04670.00430.01690.0214-0.01440.0516-0.01590.038419.64265.02221.053
20.4167-0.18790.01260.53880.00110.00630.05350.04660.0299-0.1085-0.0627-0.03230.0073-0.00280.00920.05820.02460.01260.03620.00630.02150.8633.84814.794
30.1204-0.1027-0.00260.2279-0.22180.61450.0008-0.003-0.0126-0.01530.0460.06060.0878-0.0455-0.04680.0385-0.02270.00680.04310.01130.050526.70933.53151.817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 330
2X-RAY DIFFRACTION1A340 - 361
3X-RAY DIFFRACTION2B16 - 361
4X-RAY DIFFRACTION3C16 - 330
5X-RAY DIFFRACTION3C340 - 361

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