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- PDB-4pq9: Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum -

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Basic information

Entry
Database: PDB / ID: 4pq9
TitleCrystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum
ComponentsBeta-1,3-glucanase
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Glycosyl hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Beta-1,3-glucanase from Mycobacterium marinum
Authors: Dranow, D.M. / Davies, D.R. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,3-glucanase
B: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6538
Polymers58,1002
Non-polymers5536
Water10,052558
1
A: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3705
Polymers29,0501
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2843
Polymers29,0501
Non-polymers2342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.120, 46.840, 51.840
Angle α, β, γ (deg.)109.450, 95.630, 99.790
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Beta-1,3-glucanase


Mass: 29049.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: MMAR_2902 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HE62
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 1.73 Å3/Da / Density % sol: 28.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MCSG1(a7): 25% PEG3350, Bis-Tris:HCl, pH=5.5, 0.2M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 121825 / Num. obs: 114838 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 12.164 Å2 / Rmerge(I) obs: 0.032 / Χ2: 0.999 / Net I/σ(I): 26.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.2-1.230.1319.5432653826491.3
1.23-1.260.11910.6131906801491.5
1.26-1.30.10511.9231366788792.2
1.3-1.340.0961330457765292.6
1.34-1.390.08414.8129746747992.9
1.39-1.430.06917.528854725793.6
1.43-1.490.06219.3827998705593.9
1.49-1.550.05422.0127068682194.5
1.55-1.620.04625.5226041657494.6
1.62-1.70.04128.1424776626595.2
1.7-1.790.03631.7923952606595.8
1.79-1.90.03135.9922457571296
1.9-2.030.02839.8520943536996.6
2.03-2.190.02643.3719629506096.9
2.19-2.40.02545.4518165467497.4
2.4-2.680.02447.2916438425297.7
2.68-3.10.02250.3414424373398.1
3.1-3.790.0252.5611861313096.8
3.79-5.370.0252.458780235894.1
5.370.02150.174506121789.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3rq0

3rq0


Resolution: 1.2→48.2 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1512 / WRfactor Rwork: 0.1237 / FOM work R set: 0.9295 / SU B: 0.882 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0369 / SU Rfree: 0.0359 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1435 5619 4.9 %RANDOM
Rwork0.1176 ---
obs0.1189 114838 94.38 %-
all-120457 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.25 Å2 / Biso mean: 10.217 Å2 / Biso min: 2.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.08 Å20.19 Å2
2---0.24 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3696 0 35 558 4289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024021
X-RAY DIFFRACTIONr_bond_other_d0.0010.023490
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9055535
X-RAY DIFFRACTIONr_angle_other_deg0.80438028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1225511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72922.913206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5851533
X-RAY DIFFRACTIONr_chiral_restr0.1020.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021064
X-RAY DIFFRACTIONr_mcbond_it1.2220.8471910
X-RAY DIFFRACTIONr_mcbond_other1.2220.8471909
X-RAY DIFFRACTIONr_mcangle_it1.6131.282396
X-RAY DIFFRACTIONr_rigid_bond_restr1.65537511
X-RAY DIFFRACTIONr_sphericity_free29.8965148
X-RAY DIFFRACTIONr_sphericity_bonded7.6157763
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.135 411 -
Rwork0.107 7837 -
all-8248 -
obs--91.25 %

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