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- PDB-5i0f: Cycloalternan-degrading enzyme from Trueperella pyogenes in compl... -

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Basic information

Entry
Database: PDB / ID: 5i0f
TitleCycloalternan-degrading enzyme from Trueperella pyogenes in complex with covalent intermediate
ComponentsGlycoside hydrolase family 31
KeywordsSUGAR BINDING PROTEIN / Hydrolase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Glycoside hydrolase family 31
Similarity search - Component
Biological speciesTrueperella pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLight, S.H. / Minasov, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Structure / Year: 2017
Title: Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity.
Authors: Light, S.H. / Cahoon, L.A. / Mahasenan, K.V. / Lee, M. / Boggess, B. / Halavaty, A.S. / Mobashery, S. / Freitag, N.E. / Anderson, W.F.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,48412
Polymers82,3281
Non-polymers1,15511
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-36 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.127, 103.128, 44.094
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Glycoside hydrolase family 31


Mass: 82328.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trueperella pyogenes (bacteria) / Gene: CQ11_05330 / Production host: Escherichia coli (E. coli) / References: UniProt: X4QP62

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 618 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein solution: 8.0 mg/ml, 0.5 M NaCl, 0.01 M Tris-HCl pH 8.3 Crystallization condition: PACT (Qiagen) B11: 0.2 M Calcium chloride, 0.1 m MES pH 6, and 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 74285 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.95 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F7S

5f7s


Resolution: 1.85→28.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.021 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 3512 4.7 %RANDOM
Rwork0.15899 ---
obs0.1604 70772 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.274 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å21.52 Å2
2--0.41 Å20 Å2
3----0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.85→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 63 609 6455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196030
X-RAY DIFFRACTIONr_bond_other_d0.0020.025402
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9378231
X-RAY DIFFRACTIONr_angle_other_deg1.028312414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03623.125304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87715871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8431551
X-RAY DIFFRACTIONr_chiral_restr0.0990.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216910
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021487
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_it0.7981.9532919
X-RAY DIFFRACTIONr_mcbond_other0.7971.9522918
X-RAY DIFFRACTIONr_mcangle_it1.3392.9223647
X-RAY DIFFRACTIONr_mcangle_other1.3392.9233648
X-RAY DIFFRACTIONr_scbond_it1.0432.0793111
X-RAY DIFFRACTIONr_scbond_other1.0432.0793111
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7173.0714585
X-RAY DIFFRACTIONr_long_range_B_refined4.78616.9467355
X-RAY DIFFRACTIONr_long_range_B_other4.78616.9497356
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 283 -
Rwork0.233 5172 -
obs--99.69 %
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)
10.7032-0.70110.35988.975-4.24292.0077-0.002-0.0016-0.10210.05980.08070.1606-0.033-0.0385-0.07870.04570.01590.01630.00850.01430.047-26.699327.898617.1168
22.07350.8263-1.64091.6967-1.55684.79620.0404-0.1542-0.170.0103-0.1205-0.2308-0.04560.34970.08010.0075-0.0041-00.03970.04520.1399-17.377718.920621.0219
30.48670.1269-0.76070.9660.86682.4069-0.0588-0.1271-0.10190.0962-0.0758-0.04040.18890.14870.13460.21560.0880.0440.10110.0220.0378-30.642640.230427.7543
42.49822.0013-2.86661.9734-2.0374.4255-0.0392-0.1803-0.2731-0.1047-0.194-0.20090.11020.12440.23320.03090.01150.00310.03420.05750.1441-20.363217.078720.1451
50.9618-0.2608-0.31040.92890.07570.4178-0.0705-0.0047-0.0659-0.08740.0055-0.15740.03860.06050.06510.0491-0.00320.03390.0197-0.00580.0749-15.398945.78242.1781
68.7502-1.46152.15857.22210.95230.77960.1910.1909-0.08810.1315-0.1489-0.08410.07660.0238-0.04210.1224-0.0110.01830.04070.0120.0388-21.453326.6078-5.2855
70.9443-0.0498-0.16910.44670.10190.3773-0.02760.0335-0.0141-0.0454-0.02350.0961-0.0271-0.07830.0510.04310.0012-0.01540.0206-0.01580.031-49.381153.35235.4096
80.801-0.0477-0.01750.46640.06910.3091-0.03380.02690.0445-0.03450.0102-0.0417-0.0406-0.00180.02370.0479-0.0035-0.00920.0023-0.00290.0218-36.396358.21436.6272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 19
2X-RAY DIFFRACTION2B20 - 63
3X-RAY DIFFRACTION3B64 - 87
4X-RAY DIFFRACTION4B88 - 130
5X-RAY DIFFRACTION5B131 - 254
6X-RAY DIFFRACTION6B255 - 261
7X-RAY DIFFRACTION7B262 - 397
8X-RAY DIFFRACTION8B398 - 732

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