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- PDB-5c8q: Crystal structure of MoCVNH3 variant (Mo0v) in complex with (N-Gl... -

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Basic information

Entry
Database: PDB / ID: 5c8q
TitleCrystal structure of MoCVNH3 variant (Mo0v) in complex with (N-GlcNAc)4
ComponentsMoCVNH3 variant
KeywordsSUGAR BINDING PROTEIN / lectin / N-acetylglucosamine / CVNH
Function / homology
Function and homology information


Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH ...Glycine zipper 2TM domain / Glycine zipper 2TM domain / Membrane-bound Lytic Murein Transglycosylase D; Chain A / LysM domain / HIV-inactivating Protein, Cyanovirin-n / Cyanovirin-N / Cyanovirin-N / Cyanovirin-N superfamily / CVNH domain / CVNH / Lysin motif / LysM domain superfamily / LysM domain profile. / LysM domain / LysM domain / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LysM domain-containing protein / LysM domain-containing protein
Similarity search - Component
Biological speciesMagnaporthe oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKoharudin, L.M.I. / Gronenborn, A.M.
CitationJournal: Structure / Year: 2015
Title: Structural Insight into Fungal Cell Wall Recognition by a CVNH Protein with a Single LysM Domain.
Authors: Koharudin, L.M. / Debiec, K.T. / Gronenborn, A.M.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MoCVNH3 variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1772
Polymers17,3461
Non-polymers8311
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.720, 50.277, 43.132
Angle α, β, γ (deg.)90.00, 103.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MoCVNH3 variant


Mass: 17345.996 Da / Num. of mol.: 1 / Fragment: UNP residues 175-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: L7JBY8, UniProt: G4N991*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: ~8-10 % (w/v) PEG 3350, 0.1 M sodium phosphate-citrate buffer, pH 4.2, 0.2 M NaCl
PH range: 4.2-5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 3, 2011
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→41.94 Å / Num. obs: 11980 / % possible obs: 98.7 % / Redundancy: 4.03 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.51 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.2 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
d*TREKdata reduction
Cootmodel building
PHASERphasing
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L5B,1Y7M

1l5b

1y7m


Resolution: 1.9→41.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.026 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25583 1180 9.8 %RANDOM
Rwork0.2235 ---
obs0.22677 10800 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.178 Å2
Baniso -1Baniso -2Baniso -3
1--13.77 Å2-0 Å2-4.1 Å2
2---2.91 Å2-0 Å2
3---16.69 Å2
Refinement stepCycle: 1 / Resolution: 1.9→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 57 94 1352
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211282
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.9741735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7455150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9122.70374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.6815196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9251518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021007
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6051.5737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04221169
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8243545
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8454.5566
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
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 81 -
Rwork0.242 792 -
obs--96.78 %

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