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- PDB-5vg0: Room temperature X-ray crystallographic structure of a Jonesia de... -

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Basic information

Entry
Database: PDB / ID: 5vg0
TitleRoom temperature X-ray crystallographic structure of a Jonesia denitrificans lytic polysaccharide monooxygenase at 1.1 angstrom resolution.
ComponentsChitinase
KeywordsSUGAR BINDING PROTEIN / histidine brace / HYDROLASE
Function / homology
Function and homology information


endochitinase activity / chitinase / chitin catabolic process / chitin binding / carbohydrate binding / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
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 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...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 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Immunoglobulin E-set / Glycoside hydrolase superfamily
Similarity search - Domain/homology
COPPER (II) ION / PEROXIDE ION / chitinase
Similarity search - Component
Biological speciesJonesia denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsBacik, J.-P. / Unkefer, C.J. / Chen, J.C.H.
CitationJournal: Biochemistry / Year: 2017
Title: Neutron and Atomic Resolution X-ray Structures of a Lytic Polysaccharide Monooxygenase Reveal Copper-Mediated Dioxygen Binding and Evidence for N-Terminal Deprotonation.
Authors: Bacik, J.P. / Mekasha, S. / Forsberg, Z. / Kovalevsky, A.Y. / Vaaje-Kolstad, G. / Eijsink, V.G.H. / Nix, J.C. / Coates, L. / Cuneo, M.J. / Unkefer, C.J. / Chen, J.C.
History
DepositionApr 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr3_auth_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.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Nov 13, 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: Chitinase
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2776
Polymers31,0862
Non-polymers1914
Water5,386299
1
A: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6383
Polymers15,5431
Non-polymers962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6383
Polymers15,5431
Non-polymers962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.040, 75.560, 120.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chitinase


Mass: 15542.896 Da / Num. of mol.: 2 / Fragment: residues 32-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jonesia denitrificans (strain ATCC 14870 / DSM 20603 / CIP 55134) (bacteria)
Strain: ATCC 14870 / DSM 20603 / CIP 55134 / Gene: Jden_1381 / Production host: Escherichia coli (E. coli) / References: UniProt: C7R4I0, chitinase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with ...Details: Purified enzyme was incubated with a threefold molar excess of CuSO4 for 30 min at room temperature. To remove excess copper, the protein was loaded onto a desalting column equilibrated with 20 mM Tris-HCl pH 8.0. 30 ul protein solution at 48 mg/ml was mixed with 30 ul reservoir buffer consisting of 1.9 M DL-malic acid pH 7.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→32 Å / Num. obs: 1248110 / % possible obs: 97.3 % / Redundancy: 10.7 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 10.4 % / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AA7

5aa7


Resolution: 1.1→32 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.51
RfactorNum. reflection% reflection
Rfree0.128 2000 1.72 %
Rwork0.114 --
obs0.114 116060 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.1→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 0 6 299 2493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082370
X-RAY DIFFRACTIONf_angle_d0.9753285
X-RAY DIFFRACTIONf_dihedral_angle_d16.245869
X-RAY DIFFRACTIONf_chiral_restr0.079365
X-RAY DIFFRACTIONf_plane_restr0.007463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.12750.27071370.24567807X-RAY DIFFRACTION95
1.1275-1.1580.20741380.21437851X-RAY DIFFRACTION95
1.158-1.19210.23211390.19937906X-RAY DIFFRACTION95
1.1921-1.23060.18841390.17997929X-RAY DIFFRACTION95
1.2306-1.27450.15771400.15468005X-RAY DIFFRACTION96
1.2745-1.32560.14141410.13018025X-RAY DIFFRACTION97
1.3256-1.38590.15291410.11348090X-RAY DIFFRACTION97
1.3859-1.4590.13251440.10158151X-RAY DIFFRACTION97
1.459-1.55040.10491430.08888211X-RAY DIFFRACTION98
1.5504-1.67010.11511450.08538284X-RAY DIFFRACTION99
1.6701-1.83810.09921460.08628297X-RAY DIFFRACTION99
1.8381-2.10410.09021480.0858439X-RAY DIFFRACTION99
2.1041-2.65070.111500.10298517X-RAY DIFFRACTION100
2.6507-32.01080.12891490.11378548X-RAY DIFFRACTION96

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