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- PDB-6pv4: Structure of CpGH84A -

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Basic information

Entry
Database: PDB / ID: 6pv4
TitleStructure of CpGH84A
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homology
Function and homology information


hyaluronoglucosaminidase / hyalurononglucosaminidase activity / organonitrogen compound metabolic process / carbohydrate derivative metabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / metal ion binding
Similarity search - Function
FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. ...FIVAR domain / : / Hyaluronidase post-catalytic domain-like / Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Coagulation factor 5/8 C-terminal domain, discoidin domain / Dockerin domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Glycosyl hydrolase, all-beta / Galactose-binding-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Hyaluronoglucosaminidase
Similarity search - Component
Biological speciesClostridium perfringens ATCC 13124 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Glycobiology / Year: 2019
Title: Structural and functional analysis of four family 84 glycoside hydrolases from the opportunistic pathogen Clostridium perfringens.
Authors: Pluvinage, B. / Massel, P.M. / Burak, K. / Boraston, A.B.
History
DepositionJul 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoside Hydrolase
B: Glycoside Hydrolase
C: Glycoside Hydrolase
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,41546
Polymers296,2264
Non-polymers2,18942
Water30,9501718
1
A: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,61111
Polymers74,0561
Non-polymers55510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60712
Polymers74,0561
Non-polymers55111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,69113
Polymers74,0561
Non-polymers63512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,50510
Polymers74,0561
Non-polymers4499
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.090, 92.110, 103.080
Angle α, β, γ (deg.)95.740, 110.520, 119.710
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glycoside Hydrolase /


Mass: 74056.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens ATCC 13124 (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: nagH, CPF_0184 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YRL1, hyaluronoglucosaminidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1718 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 0.15 M CaCl2 and 20 mM octyl-beta-D-glucopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97965 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.2→78 Å / Num. obs: 129154 / % possible obs: 98.1 % / Redundancy: 2.7 % / CC1/2: 0.929 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.113 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 18702 / CC1/2: 0.454 / Rpim(I) all: 0.262 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V5C

2v5c


Resolution: 2.2→75.45 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.096 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.332 / ESU R Free: 0.231 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 6401 5 %RANDOM
Rwork0.2019 ---
obs0.2042 122753 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.31 Å2 / Biso mean: 14.599 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-1.25 Å20.25 Å2
2--0.43 Å2-0.45 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.2→75.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19047 0 111 1727 20885
Biso mean--24.43 19.68 -
Num. residues----2406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01219611
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.63426586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51352400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38824.6311110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.187153090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0971564
X-RAY DIFFRACTIONr_chiral_restr0.0940.22492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215519
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 455 -
Rwork0.22 9037 -
all-9492 -
obs--97.23 %

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