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

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Basic information

Entry
Database: PDB / ID: 5hpo
TitleCycloalternan-forming enzyme from Listeria monocytogenes in complex with maltopentaose
ComponentsLmo2446 protein
KeywordsHYDROLASE / lmo2446 / Listeria monocytogenes EGD-e / Center for Structural Genomics of Infectious Diseases / CSGID / SUGAR BINDING PROTEIN
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
alpha-maltotriose / alpha-maltotetraose / DI(HYDROXYETHYL)ETHER / Lmo2446 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 20, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_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: Lmo2446 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,62410
Polymers122,5201
Non-polymers2,1039
Water22,6811259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-26 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.646, 100.131, 73.281
Angle α, β, γ (deg.)90.00, 105.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2282-

HOH

21A-2428-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lmo2446 protein


Mass: 122520.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2446 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8Y4J2

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Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1265 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1259 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 7.3 mg/mL in 500 mM NaCl, 10 mM Tris pH 8.3, 5 mM BME Crystallization: 200 mM magnesium formate and 25% PEG 3350 Soak: crystallization condition plus + 10 mM maltopentaose

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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: BeLenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 103966 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.37
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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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: 1.8→29.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.696 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16381 5194 5 %RANDOM
Rwork0.13313 ---
obs0.13465 98699 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.214 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.27 Å2
2--0.24 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 103 1259 9697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.028901
X-RAY DIFFRACTIONr_bond_other_d0.0010.027700
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.95312179
X-RAY DIFFRACTIONr_angle_other_deg0.782317851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.52651118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78525.661454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.027151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4111525
X-RAY DIFFRACTIONr_chiral_restr0.0950.21307
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022066
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 373 -
Rwork0.174 7027 -
obs--96.78 %
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)
11.4824-0.42110.07261.1528-0.4561.9384-0.0689-0.18050.08140.20640.0572-0.0865-0.25440.07660.01160.1201-0.04670.00740.0611-0.02480.0188-38.223711.228150.1939
20.5205-0.23560.071.0507-0.32490.7347-0.0474-0.04690.07140.14870.06970.1392-0.1516-0.1454-0.02230.08920.02140.04510.054-0.00320.0852-63.806128.61924.76
30.44970.05520.0110.394-0.0340.47170.0072-0.0079-0.00380.0211-0.0259-0.0384-0.03390.12540.01870.0211-0.028-0.00380.05930.01810.022-35.93618.52413.6716
40.560.20380.13210.37580.08650.5116-0.0290.086-0.011-0.07360.0302-0.00410.0140.0488-0.00110.0263-0.0145-0.00170.0350.00890.0111-53.1712-2.7217-3.8601
51.25970.544-0.0150.43530.21730.7015-0.13950.27690.0588-0.21470.12790.0524-0.17560.16350.01160.1362-0.0462-0.02950.15560.02080.011-62.5127-2.1645-25.5953
61.0348-0.0656-0.1851.20050.7321.26030.00920.1111-0.0686-0.0554-0.09280.10320.0625-0.07630.08360.0180.0136-0.00760.0493-0.01810.0241-81.0452-15.8252-18.135
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 113
2X-RAY DIFFRACTION2A114 - 245
3X-RAY DIFFRACTION3A246 - 601
4X-RAY DIFFRACTION4A602 - 870
5X-RAY DIFFRACTION5A871 - 948
6X-RAY DIFFRACTION6A949 - 1060

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