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- PDB-2zez: Family 16 Carbohydrate Binding Module-2 -

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Basic information

Entry
Database: PDB / ID: 2zez
TitleFamily 16 Carbohydrate Binding Module-2
ComponentsS-layer associated multidomain endoglucanase
KeywordsHYDROLASE / Family 16 carbohydrate binding module-2 / Glycosidase
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 speciesThermoanaerobacterium polysaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBae, B. / Nair, S.K.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Molecular Basis for the Selectivity and Specificity of Ligand Recognition by the Family 16 Carbohydrate-binding Modules from Thermoanaerobacterium polysaccharolyticum ManA
Authors: Bae, B. / Ohene-Adjei, S. / Kocherginskaya, S. / Mackie, R.I. / Spies, M.A. / Cann, I.K. / Nair, S.K.
History
DepositionDec 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: S-layer associated multidomain endoglucanase
B: S-layer associated multidomain endoglucanase
C: S-layer associated multidomain endoglucanase
D: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3028
Polymers63,1424
Non-polymers1604
Water4,738263
1
A: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8262
Polymers15,7861
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8262
Polymers15,7861
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8262
Polymers15,7861
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: S-layer associated multidomain endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8262
Polymers15,7861
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.425, 99.525, 139.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
S-layer associated multidomain endoglucanase / Family 16 CBM-2


Mass: 15785.535 Da / Num. of mol.: 4 / Fragment: CBM-2, UNP residues 756-899
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium polysaccharolyticum (bacteria)
Gene: celA / Plasmid: pET-28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZA17
#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.5M sodium formate pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51462 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.037 / Net I/σ(I): 35.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 11.6 / Num. unique all: 4669 / Rsym value: 0.169 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZEW

2zew


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.041 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27203 2607 5.1 %RANDOM
Rwork0.2326 ---
obs0.23459 48583 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.141 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2---1.2 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4409 0 4 263 4676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9266194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.46125.577208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.277154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2657
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023544
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21904
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23099
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.278
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.52884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91324501
X-RAY DIFFRACTIONr_scbond_it1.48532005
X-RAY DIFFRACTIONr_scangle_it2.0894.51693
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
Rfree0.262 177 -
Rwork0.245 3284 -
obs--86.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0279-0.27180.14773.96920.71181.17250.07850.1987-0.0934-0.5045-0.21380.6561-0.0893-0.14060.1354-0.11980.0261-0.0682-0.0962-0.0896-0.15127.1152-6.8208-18.7398
23.64980.80980.41512.4625-0.22561.2243-0.29450.21680.6098-0.25710.07420.0642-0.1420.0310.2203-0.0788-0.0053-0.0748-0.12870.0635-0.129842.639622.8238-18.3136
33.0733-0.5708-0.36462.55240.61521.3768-0.02430.2956-0.7432-0.1693-0.0083-0.12140.1156-0.01680.0325-0.09390.00930.1281-0.1103-0.04990.01536.836927.3591-19.0657
42.7374-0.0992-0.30723.04330.75881.4277-0.022-0.120.0440.1517-0.24540.95880.0169-0.24050.2674-0.0714-0.00620.1452-0.1062-0.12830.177727.037.2705-51.6155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1433 - 143
2X-RAY DIFFRACTION2BB3 - 1433 - 143
3X-RAY DIFFRACTION3CC3 - 1433 - 143
4X-RAY DIFFRACTION4DD3 - 1433 - 143

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