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- PDB-4kwu: 1.9 Angstrom resolution crystal structure of uncharacterized prot... -

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Entry
Database: PDB / ID: 4kwu
Title1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e in complex with alpha-D-glucose, beta-D-glucose, magnesium and calcium
ComponentsLmo2446 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / TIM-barrel / beta-fold
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Lmo2446-like, N-terminal / : / : / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Carbohydrate binding module (family 6) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain ...Lmo2446-like, N-terminal / : / : / Carbohydrate binding module (family 35) / glycosyl hydrolase (family 31) / Carbohydrate binding module (family 6) / 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 / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
beta-D-glucopyranose / alpha-D-glucopyranose / Lmo2446 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e in complex with alpha-D-glucose, beta-D-glucose, magnesium and calcium
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 1.3Sep 20, 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 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
A: Lmo2446 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,55620
Polymers122,5201
Non-polymers2,03619
Water22,1941232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)166.125, 102.962, 75.006
Angle α, β, γ (deg.)90.00, 104.93, 90.00
Int Tables number5
Space group name H-MC121

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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 / Fragment: UNP residues 31-1091
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: 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, 10 molecules

#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1241 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: crystallization conditions - 0.2 M magnesium formate, 20% (w/v) PEG3350 (The JCSG+ suite: A5), protein - 7.3 mg/mL in 10 mM Tris-HCl pH8.3 500 mM NaCl 5 mM BME, soak/cryo - crystallization ...Details: crystallization conditions - 0.2 M magnesium formate, 20% (w/v) PEG3350 (The JCSG+ suite: A5), protein - 7.3 mg/mL in 10 mM Tris-HCl pH8.3 500 mM NaCl 5 mM BME, soak/cryo - crystallization conditions + 50% glucose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0782 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2013 / Details: Mirror
RadiationMonochromator: Si(111)Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0782 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 94351 / Num. obs: 94351 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4671 / % possible all: 97.5

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KMQ

4kmq


Resolution: 1.9→29.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.408 / SU ML: 0.072 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17075 4730 5 %RANDOM
Rwork0.13508 ---
obs0.13686 89621 98.36 %-
all-89621 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.468 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å21.82 Å2
2--0.2 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 129 1232 9696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228918
X-RAY DIFFRACTIONr_bond_other_d0.0010.025697
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.94312201
X-RAY DIFFRACTIONr_angle_other_deg0.872313947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.41751117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.06225.6450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.189151357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0471525
X-RAY DIFFRACTIONr_chiral_restr0.0960.21321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021816
X-RAY DIFFRACTIONr_mcbond_it0.7291.55428
X-RAY DIFFRACTIONr_mcbond_other0.2311.52223
X-RAY DIFFRACTIONr_mcangle_it1.29428792
X-RAY DIFFRACTIONr_scbond_it2.33533490
X-RAY DIFFRACTIONr_scangle_it3.5894.53409
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 312 -
Rwork0.193 6450 -
obs-6450 95.27 %
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)
11.3418-0.42190.31051.0319-0.16361.145-0.0221-0.1588-0.00220.06680.0523-0.0724-0.0344-0.0198-0.03020.0717-0.0236-0.00850.0313-0.00550.029542.997259.789851.2843
20.6944-0.1469-0.01010.9427-0.27061.3769-0.0013-0.0230.11870.0310.03140.05-0.1261-0.0962-0.03020.06490.01340.00950.0094-0.01120.104419.365578.86425.5101
30.47550.04950.00470.26050.08460.3826-0.00380.01450.00660.01750.0074-0.0372-0.02230.0714-0.00370.0451-0.0176-0.01590.01950.01140.035945.889956.849415.4618
40.57030.06640.10050.33750.03240.4120.0070.0673-0.0362-0.02280.0075-0.01240.02790.0109-0.01450.025-0.0083-0.01330.01240.00270.01429.590244.6603-0.6696
51.49980.2815-0.05650.6957-0.20130.72470.00040.34330.0628-0.14990.01020.0158-0.02420.1162-0.01050.06510.0002-0.01530.14490.02360.015121.243451.0366-24.7607
62.1427-0.5328-0.49841.50170.37450.99240.0178-0.0005-0.0681-0.0857-0.05290.0630.1245-0.01770.0350.04290.0104-0.0170.0269-0.01980.02541.828833.0871-16.638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 144
2X-RAY DIFFRACTION2A145 - 271
3X-RAY DIFFRACTION3A272 - 632
4X-RAY DIFFRACTION4A633 - 875
5X-RAY DIFFRACTION5A876 - 972
6X-RAY DIFFRACTION6A973 - 1091

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