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- PDB-5hxm: Cycloalternan-forming enzyme from Listeria monocytogenes in compl... -

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Basic information

Entry
Database: PDB / ID: 5hxm
TitleCycloalternan-forming enzyme from Listeria monocytogenes in complex with panose
ComponentsAlpha-xylosidase
KeywordsHYDROLASE / Center for Structural Genomics of Infectious Diseases / CSGID / idp05250 / lmo2446 / Listeria monocytogenes EGD-e
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. ...: / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHalavaty, A.S. / Light, S.H. / Minasov, G. / Winsor, J. / Grimshaw, S. / Shuvalova, L. / Peterson, S. / 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
DepositionJan 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,76211
Polymers122,5201
Non-polymers1,24110
Water18,4651025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-25 kcal/mol
Surface area37130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.157, 102.437, 74.011
Angle α, β, γ (deg.)90.00, 103.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2167-

HOH

21A-2213-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-xylosidase / Glycosyl hydrolase family 31


Mass: 122520.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: yicI_4, ABE87_12155, ARD00_02746 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: A0A0R1CZZ2, UniProt: Q8Y4J2*PLUS, alpha-D-xyloside xylohydrolase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2/a1-d6_a3-b1_b6-c1_c3-d1WURCSPDB2Glycan 1.1.0
#3: 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

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Non-polymers , 4 types, 1033 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1025 / 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: 2.56 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 0.5 NaCl, 10 mM Tris pH 8.3, 5 mM BME Crystallization: 200 mM magnesium formate and 25% PEG 3350 Soak for 1 minute in reservoir + 5 mM panose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 14, 2014 / Details: Be-Lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 94486 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kmq

4kmq


Resolution: 1.9→29.74 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 8.187 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19495 4728 5 %RANDOM
Rwork0.15219 ---
obs0.15433 89736 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.394 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å25.33 Å2
2---4.81 Å2-0 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.9→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8343 0 75 1025 9443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028779
X-RAY DIFFRACTIONr_bond_other_d0.0010.027614
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9511986
X-RAY DIFFRACTIONr_angle_other_deg0.792317589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.30251097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06325.603448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.175151237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.651525
X-RAY DIFFRACTIONr_chiral_restr0.0980.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022043
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
Rfree0.327 361 -
Rwork0.291 6497 -
obs--98.24 %
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)
11.3532-0.335-0.0282.3618-0.10731.14360.1106-0.17290.03480.4264-0.0379-0.052-0.05630.0615-0.07270.2558-0.0646-0.10950.2373-0.0270.0875-38.21978.360250.8438
20.62750.06810.18931.0038-0.34591.1138-0.0383-0.04320.08170.16670.08740.1571-0.1726-0.0979-0.04910.07330.0271-0.01680.06290.00150.083-63.00327.183125.4329
30.29280.01450.01170.91010.21450.47890.04190.020.0355-0.00850.0757-0.1957-0.0260.127-0.11770.0803-0.0232-0.06770.2081-0.01780.1464-40.98151.22311.1127
42.9489-1.1802-2.8481.0894-0.02956.720.15830.23910.0862-0.16850.00390.1742-0.1165-0.2784-0.16220.1533-0.0351-0.1420.3150.01360.2049-68.4567-8.631-2.9362
51.192-0.1329-0.13050.8164-0.05790.76840.17220.35940.1533-0.3149-0.0214-0.0133-0.0786-0.0353-0.15080.28110.024-0.08550.4090.05390.1519-58.6473-0.9155-20.5319
62.3715-0.5081-1.3731.91910.74531.1402-0.0330.0164-0.1541-0.0712-0.0425-0.05260.0405-0.02960.07550.21240.0336-0.19070.4149-0.00420.2107-81.4287-18.0806-16.9859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 143
2X-RAY DIFFRACTION2A144 - 271
3X-RAY DIFFRACTION3A272 - 785
4X-RAY DIFFRACTION4A786 - 812
5X-RAY DIFFRACTION5A813 - 968
6X-RAY DIFFRACTION6A969 - 1091

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