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- PDB-5hop: 1.65 Angstrom resolution crystal structure of lmo0182 (residues 1... -

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Basic information

Entry
Database: PDB / ID: 5hop
Title1.65 Angstrom resolution crystal structure of lmo0182 (residues 1-245) from Listeria monocytogenes EGD-e
ComponentsLmo0182 protein
KeywordsHYDROLASE / lmo0182 / Center for Structural Genomics of Infectious Diseases / CSGID / Listeria monocytogenes EGD-e
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 / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily ...: / 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 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / Lmo0182 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsHalavaty, A.S. / Light, S.H. / Minasov, G. / Grimshaw, S. / Kwon, K. / 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 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0182 protein
B: Lmo0182 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1244
Polymers57,0062
Non-polymers1182
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-0 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.141, 110.141, 45.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 239 / Label seq-ID: 4 - 242

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Lmo0182 protein


Mass: 28503.094 Da / Num. of mol.: 2 / Mutation: UNP residues 2-245
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: lmo0182 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8YAE8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: protein: 15.2 mg/ml in 10 mM Tris-HCl pH 8.3 0.5 mM TCEP crystallization: The PACT Suite C2(#26): 0.1 M PCB buffer pH 5.0 25% (w/v) PEG1500 cryo: crystallization condition

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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: Aug 13, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 65420 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 44.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→29.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.655 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19449 3307 5.1 %RANDOM
Rwork0.16245 ---
obs0.16404 62015 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.295 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0 Å2
2---1.2 Å2-0 Å2
3---2.41 Å2
Refinement stepCycle: 1 / Resolution: 1.65→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 0 8 612 4436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194074
X-RAY DIFFRACTIONr_bond_other_d0.0020.023913
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9925540
X-RAY DIFFRACTIONr_angle_other_deg0.8639061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3845514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14925.568176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.26315671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.3541512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02886
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 16002 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 246 -
Rwork0.224 4540 -
obs--100 %
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)
11.1598-0.8781-0.0933.161-0.16420.34320.08230.0383-0.1147-0.3427-0.05870.24410.016-0.0045-0.02360.12050.0238-0.02270.0964-0.01160.022953.704821.024116.1003
20.9558-0.6389-0.20221.770.05191.30350.02050.01870.0558-0.0893-0.05160.0123-0.0850.04640.03110.09940.0130.0110.08520.00640.009651.86940.059621.2718
32.7309-0.13860.09264.0418-0.31582.481-0.0818-0.1342-0.02650.34420.07430.3307-0.1013-0.0510.00760.13070.0330.04670.12140.00740.031544.934.846234.9435
45.70840.25190.65665.28230.25475.3167-0.0957-0.2082-0.33420.34190.01820.08860.20010.21060.07740.16010.04220.08360.11660.03270.058948.912924.298535.6677
53.1398-0.8333-0.19341.1704-0.07780.401-0.0568-0.34460.25450.04760.0848-0.1191-0.00040.0144-0.0280.09550.0255-0.01220.1245-0.02340.025134.05021.363540.2981
62.5023-0.2157-0.16350.9158-0.2551.7212-0.063-0.10310.05490.03650.02930.11840.0521-0.09690.03370.08920.02070.00980.10150.01040.023815.80742.213636.4908
74.2211-0.3844-0.50571.5545-0.40451.75450.05590.30280.2828-0.1442-0.0386-0.0717-0.0187-0.0905-0.01730.11690.02920.00650.11770.03990.024718.57849.720622.5054
84.97770.40430.2516.5241.13155.39170.01650.2940.1779-0.2285-0.0873-0.3840.07160.23760.07080.11140.04550.04230.16620.08540.063330.69336.821120.5028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 117
2X-RAY DIFFRACTION2A118 - 171
3X-RAY DIFFRACTION3A172 - 218
4X-RAY DIFFRACTION4A219 - 239
5X-RAY DIFFRACTION5B1 - 117
6X-RAY DIFFRACTION6B118 - 163
7X-RAY DIFFRACTION7B164 - 217
8X-RAY DIFFRACTION8B218 - 239

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