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- PDB-5l2v: Catalytic domain of LPMO Lmo2467 from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 5l2v
TitleCatalytic domain of LPMO Lmo2467 from Listeria monocytogenes
ComponentsChitin-binding protein
KeywordsCHITIN-BINDING PROTEIN / Lytic polysaccharide monooxygenase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chitin catabolic process / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Coagulation Factor XIII; Chain A, domain 1 / Fibronectin type III domain ...chitin-binding protein cbp21 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Coagulation Factor XIII; Chain A, domain 1 / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Distorted Sandwich / Immunoglobulin E-set / Immunoglobulin-like fold / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Chitin-binding protein
Similarity search - Component
Biological speciesListeria monocytogenes serotype 1/2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsLight, S.H. / Agostoni, M. / Marletta, M.A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Catalytic domain of LPMO Lmo2467 from Listeria monocytogenes
Authors: Light, S.H. / Agostoni, M. / Marletta, M.A. / Anderson, W.F.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin-binding protein
B: Chitin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2435
Polymers35,7902
Non-polymers4533
Water11,169620
1
A: Chitin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2853
Polymers17,8951
Non-polymers3902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9582
Polymers17,8951
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.575, 139.712, 90.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-202-

P33

21A-586-

HOH

31A-637-

HOH

41A-676-

HOH

51A-763-

HOH

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Components

#1: Protein Chitin-binding protein


Mass: 17894.906 Da / Num. of mol.: 2 / Fragment: UNP residues 28-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 1/2a (strain 10403S) (bacteria)
Strain: 10403S / Gene: LMRG_01781 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0H3GIZ6
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.0 mg/ml, 0.01 M Tris HCl (pH 8.3); Screen: JCSG+ H9 (Qiagen),0.2 M AmSO4, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 148923 / % possible obs: 94.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 1.6 / % possible all: 66.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEM

2bem


Resolution: 1.1→29.15 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.824 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 7382 5 %RANDOM
Rwork0.129 ---
obs0.129 141504 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 24 620 3178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192776
X-RAY DIFFRACTIONr_bond_other_d0.0020.022560
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9543811
X-RAY DIFFRACTIONr_angle_other_deg0.92635947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6095366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23825.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.95115420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.085158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213278
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02614
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_it0.5250.7331416
X-RAY DIFFRACTIONr_mcbond_other0.5230.7331415
X-RAY DIFFRACTIONr_mcangle_it0.6991.1091798
X-RAY DIFFRACTIONr_mcangle_other0.6991.1091799
X-RAY DIFFRACTIONr_scbond_it0.7510.8621360
X-RAY DIFFRACTIONr_scbond_other0.7480.8621360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8771.2432014
X-RAY DIFFRACTIONr_long_range_B_refined3.1499.5973702
X-RAY DIFFRACTIONr_long_range_B_other1.7667.1133240
X-RAY DIFFRACTIONr_rigid_bond_restr0.93935336
X-RAY DIFFRACTIONr_sphericity_free27.4155119
X-RAY DIFFRACTIONr_sphericity_bonded6.3455763
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 476 -
Rwork0.283 8676 -
obs--80.06 %
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)
10.3955-0.0068-0.13050.74180.00730.4287-0.0076-0.0243-0.00270.02930.01320.0484-0.0199-0.0018-0.00560.0084-0.00050.00260.00270.00050.036621.952956.728743.4345
20.32480.1172-0.2520.8134-0.26020.4802-0.00830.0164-0.0381-0.05850.00640.05680.005-0.00710.00190.0161-0.004-0.00170.0049-0.00240.038722.669949.159135.5763
31.80460.4515-0.34540.602-0.23560.474-0.01150.0353-0.0086-0.00910.00730.0364-0.00720.01850.00410.00730.00090.00160.0053-0.0010.047722.489353.164738.4542
40.85140.01220.04320.7403-0.0040.4697-0.0059-0.03710.12110.05310.0132-0.0306-0.0347-0.0053-0.00730.00640.0014-0.00410.0019-0.00490.058451.87252.264449.3459
50.7892-0.147-0.05550.68320.09450.3144-0.0103-0.06750.02290.09890.0167-0.03630.0218-0.0004-0.00640.01490.0012-0.00460.00680.00360.047451.505843.631351.6653
62.7199-0.4631-0.36260.66160.06420.6424-0.037-0.11810.04230.03810.0161-0.0231-0.0327-0.01980.02090.00470.0037-0.00430.0073-0.00430.060352.213948.510650.5856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 84
2X-RAY DIFFRACTION2A85 - 149
3X-RAY DIFFRACTION3A150 - 166
4X-RAY DIFFRACTION4B1 - 102
5X-RAY DIFFRACTION5B103 - 150
6X-RAY DIFFRACTION6B151 - 166

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