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- PDB-3oea: Crystal structure of the Q121E mutants of C.polysaccharolyticus C... -

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Basic information

Entry
Database: PDB / ID: 3oea
TitleCrystal structure of the Q121E mutants of C.polysaccharolyticus CBM16-1 bound to cellopentaose
ComponentsS-layer associated multidomain endoglucanase
KeywordsHYDROLASE / Carbohydrate Binding Domain / Cellopentaose
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
: / S-layer homology domain / S-layer homology domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...: / S-layer homology domain / S-layer homology domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / S-layer homology (SLH) domain profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
S-layer associated multidomain endoglucanase
Similarity search - Component
Biological speciesCaldanaerobius polysaccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsAgarwal, V. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Mutational insights into the roles of amino acid residues in ligand binding for two closely related family 16 carbohydrate binding modules.
Authors: Su, X. / Agarwal, V. / Dodd, D. / Bae, B. / Mackie, R.I. / Nair, S.K. / Cann, I.K.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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
A: S-layer associated multidomain endoglucanase
B: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8396
Polymers32,1022
Non-polymers1,7384
Water8,953497
1
A: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9203
Polymers16,0511
Non-polymers8692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9203
Polymers16,0511
Non-polymers8692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • defined by software
TypeNameSymmetry operationNumber
crystal symmetry operation1_655x+1,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.393, 48.375, 48.985
Angle α, β, γ (deg.)62.50, 85.11, 86.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein S-layer associated multidomain endoglucanase


Mass: 16050.784 Da / Num. of mol.: 2 / Fragment: UNP residues 614-756 / Mutation: Q121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobius polysaccharolyticus (bacteria)
Gene: celA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZA17
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 30% PEG 3350, 100 mM Tris-HCl, 200 mM MgCl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→25 Å / Num. all: 54672 / Num. obs: 54672 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 45.9
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 9.4 / Num. unique all: 2632 / % possible all: 91.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0056refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ZEX

2zex


Resolution: 1.35→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.909 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20373 2769 5.1 %RANDOM
Rwork0.17464 ---
obs0.17611 51900 94.92 %-
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: 14.207 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.13 Å20.8 Å2
2---0.23 Å20.03 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 114 497 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222509
X-RAY DIFFRACTIONr_bond_other_d0.0010.021
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9883455
X-RAY DIFFRACTIONr_angle_other_deg0.78733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5426.161112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215364
X-RAY DIFFRACTIONr_chiral_restr0.0660.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211874
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022
X-RAY DIFFRACTIONr_mcbond_it0.3591.51472
X-RAY DIFFRACTIONr_mcbond_other0.1121.51
X-RAY DIFFRACTIONr_mcangle_it0.68922375
X-RAY DIFFRACTIONr_scbond_it0.96731037
X-RAY DIFFRACTIONr_scangle_it1.5234.51072
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 182 -
Rwork0.207 3672 -
obs--91.54 %

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