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- PDB-3jur: The crystal structure of a hyperthermoactive Exopolygalacturonase... -

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Basic information

Entry
Database: PDB / ID: 3jur
TitleThe crystal structure of a hyperthermoactive Exopolygalacturonase from Thermotoga maritima
ComponentsExo-poly-alpha-D-galacturonosidase
KeywordsHYDROLASE / beta-helix / Cell wall biogenesis/degradation / Glycosidase
Function / homology
Function and homology information


polygalacturonase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Exo-poly-alpha-D-galacturonosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPijning, T. / van Pouderoyen, G. / Kluskens, L.D. / van der Oost, J. / Dijkstra, B.W.
CitationJournal: Febs Lett. / Year: 2009
Title: The crystal structure of a hyperthermoactive exopolygalacturonase from Thermotoga maritima reveals a unique tetramer
Authors: Pijning, T. / van Pouderoyen, G. / Kluskens, L. / van der Oost, J. / Dijkstra, B.W.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exo-poly-alpha-D-galacturonosidase
B: Exo-poly-alpha-D-galacturonosidase
C: Exo-poly-alpha-D-galacturonosidase
D: Exo-poly-alpha-D-galacturonosidase


Theoretical massNumber of molelcules
Total (without water)202,2514
Polymers202,2514
Non-polymers00
Water20,8251156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-32 kcal/mol
Surface area62140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.274, 155.904, 200.652
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
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 5 - 448 / Label seq-ID: 5 - 448

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Exo-poly-alpha-D-galacturonosidase


Mass: 50562.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8(DSM3109) / Gene: TM0437 / Plasmid: pLUW741 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYR8, endo-polygalacturonase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1156 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-17% PEG4000, 0.1M BES-NaOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.049→123.11 Å / Num. obs: 114618 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 8.2
Reflection shellResolution: 2.049→2.102 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.8 / % possible all: 63.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UVE, 1CZF, 1NHC

2uve

1czf

1nhc


Resolution: 2.05→34.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.979 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21956 5742 5 %RANDOM
Rwork0.17509 ---
obs0.1773 108777 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.125 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14093 0 0 1156 15249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9719447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05151785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96824.077699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.927152624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.29515122
X-RAY DIFFRACTIONr_chiral_restr0.0720.22124
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110946
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_it0.3371.58812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.685214264
X-RAY DIFFRACTIONr_scbond_it1.35135590
X-RAY DIFFRACTIONr_scangle_it2.3624.55177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3491 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.425
2Bloose positional0.445
3Cloose positional0.465
4Dloose positional0.435
1Aloose thermal1.2710
2Bloose thermal1.5410
3Cloose thermal1.5110
4Dloose thermal1.2510
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 286 -
Rwork0.253 5087 -
obs--58.82 %
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)
11.57220.3448-0.9981.1236-0.4271.6481-0.0013-0.1741-0.15470.1758-0.03330.06990.0575-0.00740.03460.1125-0.01830.05480.03430.01860.084553.36643.62450.725
21.3366-0.0168-0.90760.5337-0.04611.25290.04590.0102-0.007-0.0251-0.00310.0048-0.06140.0342-0.04280.0152-0.0069-0.00230.0058-0.00380.018698.63255.2351.547
31.79550.1005-0.92641.0399-0.11411.41740.0793-0.09290.05710.0546-0.08120.1026-0.0493-0.06920.0020.0659-0.0024-0.00720.0483-0.03560.033537.39680.67548.732
41.9290.1464-0.93331.0764-0.2961.54640.04140.13910.2616-0.10220.0123-0.1397-0.19970.0705-0.05360.0862-0.03860.00830.05210.03020.06883.79592.8970.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 25
2X-RAY DIFFRACTION1A26 - 136
3X-RAY DIFFRACTION1A137 - 190
4X-RAY DIFFRACTION1A191 - 448
5X-RAY DIFFRACTION2B5 - 25
6X-RAY DIFFRACTION2B26 - 136
7X-RAY DIFFRACTION2B137 - 190
8X-RAY DIFFRACTION2B191 - 448
9X-RAY DIFFRACTION3C5 - 25
10X-RAY DIFFRACTION3C26 - 136
11X-RAY DIFFRACTION3C137 - 190
12X-RAY DIFFRACTION3C191 - 448
13X-RAY DIFFRACTION4D3 - 25
14X-RAY DIFFRACTION4D26 - 136
15X-RAY DIFFRACTION4D137 - 190
16X-RAY DIFFRACTION4D191 - 448

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