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

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Basic information

Entry
Database: PDB / ID: 4kmq
Title1.9 Angstrom resolution crystal structure of uncharacterized protein lmo2446 from Listeria monocytogenes EGD-e
ComponentsLmo2446 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / uncharacterized protein / Virulence / Pathogenesis / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / TIM-barrel
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 / : ...: / 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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHalavaty, A.S. / Minasov, G. / Filippova, E.V. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.
History
DepositionMay 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)122,7159
Polymers122,5201
Non-polymers1948
Water18,2491013
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)164.858, 102.359, 74.334
Angle α, β, γ (deg.)90.00, 104.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: crystallization conditions - The JCSG+ suite (A5: 200 mM Magnesium formate, 20 % w/v PEG3350), protein - 7.1 mg/mL in 10 mM Tris/HCl pH8.3, 500 mM NaCl, 5 mM BME, cryo - soaked in ...Details: crystallization conditions - The JCSG+ suite (A5: 200 mM Magnesium formate, 20 % w/v PEG3350), protein - 7.1 mg/mL in 10 mM Tris/HCl pH8.3, 500 mM NaCl, 5 mM BME, cryo - soaked in crystallization condition solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2013 / Details: BE-LENSES/DIAMOND LAUE MONO
RadiationMonochromator: DIAMOND[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 185978 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2 / Num. unique all: 9248 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
MLPHAREphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.66 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.318 / SU ML: 0.083 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18352 4702 5 %RANDOM
Rwork0.15103 ---
obs0.15269 88907 99.78 %-
all-88907 --
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: 30.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-0 Å20.39 Å2
2---1.61 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8327 0 8 1013 9348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228636
X-RAY DIFFRACTIONr_bond_other_d0.0010.025530
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.92811782
X-RAY DIFFRACTIONr_angle_other_deg0.84313501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.26651080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24125.563444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.28151328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181525
X-RAY DIFFRACTIONr_chiral_restr0.1020.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021778
X-RAY DIFFRACTIONr_mcbond_it0.7521.55315
X-RAY DIFFRACTIONr_mcbond_other0.2441.52185
X-RAY DIFFRACTIONr_mcangle_it1.31228580
X-RAY DIFFRACTIONr_scbond_it2.38733321
X-RAY DIFFRACTIONr_scangle_it3.6364.53202
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 325 -
Rwork0.201 6540 -
obs-6540 99.67 %
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)
12.2134-0.49930.15612.1085-0.03831.8980.1798-0.1362-0.00730.1486-0.0622-0.1045-0.13350.0444-0.11770.2-0.03030.0170.0572-0.0180.023942.889760.593550.6538
20.7436-0.46680.32152.0018-0.42891.9729-0.104-0.04160.07340.2380.16190.2377-0.1957-0.105-0.05790.13490.04150.08340.06070.00990.107119.242479.470324.76
31.0243-0.6233-0.11021.3840.2270.6301-0.0509-0.06430.1250.13510.1625-0.2284-0.02760.1778-0.11160.0297-0.0145-0.01110.0839-0.05230.049445.501757.254714.8981
41.3266-0.50950.01471.04640.1230.78690.11210.1718-0.1786-0.1387-0.02310.17080.01620.0256-0.08910.0254-0.0011-0.02970.0578-0.02260.050129.317345.0733-1.2076
53.1053-0.4369-0.50191.386-0.38181.17550.28620.8319-0.1096-0.322-0.25910.0368-0.14920.1285-0.02710.21640.1423-0.06150.4312-0.08280.040220.996851.6431-25.3193
65.39240.5437-0.53792.39770.68652.14940.20860.591-1.5022-0.0367-0.0968-0.11770.3562-0.0229-0.11180.13250.0909-0.1750.1901-0.25490.6251.3133.8745-17.2563
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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