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- PDB-3kl5: Structure Analysis of a Xylanase From Glycosyl Hydrolase Family T... -

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Basic information

Entry
Database: PDB / ID: 3kl5
TitleStructure Analysis of a Xylanase From Glycosyl Hydrolase Family Thirty: Carbohydrate Ligand Complexes Reveal this Family of Enzymes Unique Mechanism of Substrate Specificity and Recognition
ComponentsGlucuronoxylanase xynC
KeywordsHYDROLASE / alpha-beta barrel / (beta/alpha)8 barrel / (beta/alpha)8 + beta motif / dual motif hydrolase / aldotriuronic acid bound structure / aldotriuronate bound structure / XynC
Function / homology
Function and homology information


glucuronoarabinoxylan endo-1,4-beta-xylanase / glucuronoarabinoxylan endo-1,4-beta-xylanase activity / glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / extracellular region / membrane
Similarity search - Function
Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich ...Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Glucuronoxylanase XynC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsSt John, F.J. / Hurlbert, J.C. / Pozharski, E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase.
Authors: St John, F.J. / Hurlbert, J.C. / Rice, J.D. / Preston, J.F. / Pozharski, E.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification ..._pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucuronoxylanase xynC
B: Glucuronoxylanase xynC
C: Glucuronoxylanase xynC
D: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,6158
Polymers181,7264
Non-polymers1,8904
Water84747
1
A: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9042
Polymers45,4311
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3763
Polymers45,4311
Non-polymers9452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glucuronoxylanase xynC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9042
Polymers45,4311
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glucuronoxylanase xynC


Theoretical massNumber of molelcules
Total (without water)45,4311
Polymers45,4311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.723, 194.008, 65.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPVALVAL1AA4 - 804 - 80
21ASPASPVALVAL1BB4 - 804 - 80
31ASPASPVALVAL1CC4 - 804 - 80
12PHEPHEASNASN2AA81 - 11981 - 119
22PHEPHEASNASN2BB81 - 11981 - 119
32PHEPHEASNASN2CC81 - 11981 - 119
13ASPASPASNASN1AA120 - 390120 - 390
23ASPASPASNASN1BB120 - 390120 - 390
33ASPASPASNASN1CC120 - 390120 - 390

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Glucuronoxylanase xynC / Glucuronoxylan xylanohydrolase / Endoxylanase xynC


Mass: 45431.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subtilis, 168 / Gene: BSU18150, xynC, ynfF / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q45070, glucuronoarabinoxylan endo-1,4-beta-xylanase
#2: Polysaccharide
4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 472.396 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-2/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 294.6 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium tartrate, 200 mM sodium malonate, pH 7.0, 19% PEG3350 Crystal was soaked in mother liquor with cryoprotectent and aldotetrauronic acid, VAPOR DIFFUSION, SITTING DROP, temperature 294.6K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Feb 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 54718 / % possible obs: 97.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.086 / Χ2: 0.974 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.59-2.683.20.89246861.00485.4
2.68-2.794.70.851970.94394.8
2.79-2.926.20.62854720.91499.1
2.92-3.077.10.45355250.97899.9
3.07-3.267.50.28955541.014100
3.26-3.517.50.16455371.086100
3.51-3.877.40.10255900.987100
3.87-4.437.40.06555940.914100
4.43-5.587.30.05256540.978100
5.58-506.90.03559090.91699.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
Web-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KL0

3kl0


Resolution: 2.59→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 15.291 / SU ML: 0.324 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.632 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2778 5.1 %RANDOM
Rwork0.241 ---
obs0.243 54602 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 119.19 Å2 / Biso mean: 73.226 Å2 / Biso min: 23.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2--2.66 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12259 0 127 47 12433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212787
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.92617431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg651536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.12624.421656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.742151951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1971567
X-RAY DIFFRACTIONr_chiral_restr0.080.21850
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110011
X-RAY DIFFRACTIONr_mcbond_it0.5261.57672
X-RAY DIFFRACTIONr_mcangle_it1.004212377
X-RAY DIFFRACTIONr_scbond_it1.20835115
X-RAY DIFFRACTIONr_scangle_it2.0844.55054
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A594TIGHT POSITIONAL0.040.05
1B594TIGHT POSITIONAL0.040.05
1C594TIGHT POSITIONAL0.050.05
1A594TIGHT THERMAL0.10.5
1B594TIGHT THERMAL0.090.5
1C594TIGHT THERMAL0.10.5
2A156TIGHT POSITIONAL0.040.05
2B156TIGHT POSITIONAL0.040.05
2C156TIGHT POSITIONAL0.050.05
2A162MEDIUM POSITIONAL0.120.5
2B162MEDIUM POSITIONAL0.20.5
2C162MEDIUM POSITIONAL0.170.5
2A156TIGHT THERMAL0.160.5
2B156TIGHT THERMAL0.080.5
2C156TIGHT THERMAL0.180.5
2A162MEDIUM THERMAL0.152
2B162MEDIUM THERMAL0.092
2C162MEDIUM THERMAL0.172
3A2128TIGHT POSITIONAL0.070.05
3B2128TIGHT POSITIONAL0.080.05
3C2128TIGHT POSITIONAL0.090.05
3A2128TIGHT THERMAL0.140.5
3B2128TIGHT THERMAL0.130.5
3C2128TIGHT THERMAL0.140.5
LS refinement shellResolution: 2.59→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 164 -
Rwork0.394 3085 -
all-3249 -
obs--79.52 %
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)
14.4337-0.3805-0.94241.37660.38494.290.17760.67570.2550.0047-0.130.3549-0.3899-1.2392-0.04760.26740.21880.09620.79120.15770.166715.88529.633623.6583
23.7542-1.6061-1.13920.73210.81072.9421-0.252-0.60610.29270.09790.2759-0.0764-0.4217-0.4151-0.02380.6040.46740.47161.05640.36250.557717.321814.527337.147
34.61551.0587-4.79641.84550.476411.9211-0.1248-0.2123-0.13570.1409-0.28330.11310.1922-0.42540.4080.45960.08440.10570.56780.13770.196128.4691.939629.2397
40.92210.0297-2.54194.172-3.682110.8598-0.6579-0.2468-0.2892-0.10910.69430.45291.4598-0.4001-0.03650.9560.16030.33610.66460.35810.394227.7844-9.891736.2169
51.0901-2.6578-1.30386.53093.16362.98720.15650.2646-0.0546-0.7-0.89250.09241.1157-0.52650.73611.84170.04170.57140.79160.16910.671532.8209-19.056136.8556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D3 - 156
2X-RAY DIFFRACTION2D157 - 212
3X-RAY DIFFRACTION3D213 - 284
4X-RAY DIFFRACTION4D285 - 332
5X-RAY DIFFRACTION5D336 - 391

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