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- PDB-5klf: Structure of CBM_E1, a novel carbohydrate-binding module found by... -

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Basic information

Entry
Database: PDB / ID: 5klf
TitleStructure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome, complexed with cellopentaose and gadolinium ion
ComponentsCarbohydrate binding module E1
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / metagenomics / cellulose / biofuels
Function / homologybeta-cellopentaose / GADOLINIUM ATOM / Carbohydrate binding module E1
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsLiberato, M.V. / Campos, B.M. / Zeri, A.C.M. / Squina, F.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2013/06336-0 Brazil
Sao Paulo Research Foundation (FAPESP)2008/58037-9 Brazil
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties.
Authors: Campos, B.M. / Liberato, M.V. / Alvarez, T.M. / Zanphorlin, L.M. / Ematsu, G.C. / Barud, H. / Polikarpov, I. / Ruller, R. / Gilbert, H.J. / Zeri, A.C. / Squina, F.M.
History
DepositionJun 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding module E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,72814
Polymers10,0121
Non-polymers2,71613
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carbohydrate binding module E1
hetero molecules

A: Carbohydrate binding module E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,45528
Polymers20,0242
Non-polymers5,43126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area3780 Å2
ΔGint-116 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.410, 88.410, 88.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-107-

GD

21A-299-

HOH

31A-340-

HOH

41A-341-

HOH

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Components

#1: Protein Carbohydrate binding module E1


Mass: 10011.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R5P8X1
#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)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/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-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Gd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.48 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48 Å / Relative weight: 1
ReflectionResolution: 1.8→31.26 Å / Num. obs: 10827 / % possible obs: 100 % / Redundancy: 10.5 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.042 / Rrim(I) all: 0.137 / Net I/σ(I): 15.1 / Num. measured all: 113653 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8410.30.81465956410.9080.2650.8574100
9-31.269.30.0719271000.9990.0240.07524.997.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.5.2data scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.801→31.258 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1911 526 4.86 %
Rwork0.1683 10295 -
obs0.1694 10821 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.47 Å2 / Biso mean: 21.2063 Å2 / Biso min: 7.07 Å2
Refinement stepCycle: final / Resolution: 1.801→31.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms670 0 67 141 878
Biso mean--67.83 30.52 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013744
X-RAY DIFFRACTIONf_angle_d1.1811018
X-RAY DIFFRACTIONf_chiral_restr0.075127
X-RAY DIFFRACTIONf_plane_restr0.007120
X-RAY DIFFRACTIONf_dihedral_angle_d8.609389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8009-1.98210.24011540.192125282682
1.9821-2.26890.1931100.16525542664
2.2689-2.85820.20641230.176525772700
2.8582-31.26230.16831390.159426362775
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)
10.65-0.0805-0.02231.3646-0.77691.36290.03540.1181-0.01720.0443-0.0655-0.1482-0.12740.10550.02020.1189-0.01340.0040.15230.0310.134752.786142.937931.0692
24.9751.80671.30252.77230.60253.33390.0275-0.218-0.03090.2511-0.16290.0209-0.151-0.0007-0.05330.1363-0.00740.00330.14880.01160.134550.599438.587739.7162
33.2138-1.3450.72811.1588-0.41441.0435-0.06020.16760.0671-0.034-0.1978-0.3934-0.07030.34590.06930.1195-0.02110.00920.21410.07280.191958.709140.671631.3123
40.7766-0.1608-0.13541.2449-0.69421.73450.04860.02320.0256-0.1403-0.0912-0.12330.17060.27070.03990.11380.0313-0.00720.15540.01950.125656.17331.112933.472
51.68780.29280.23272.1827-0.66251.65240.07890.0111-0.1366-0.3167-0.1564-0.12680.46880.35050.09780.14850.05710.01550.20.01250.145158.826428.020534.3268
62.29770.2947-1.17882.061-1.50783.1816-0.01720.30450.2857-0.11650.1224-0.03610.08420.00170.00620.1320.0045-0.00670.18080.02390.132152.607736.652729.7958
74.42280.1273-1.23511.0527-0.79721.54440.01090.24770.03760.1406-0.0586-0.13790.00130.19010.01790.1136-0.0061-0.01560.18770.01020.09955.572533.67940.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 20 )A6 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 29 )A21 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 35 )A30 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 60 )A36 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 76 )A61 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 86 )A77 - 86
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 97 )A87 - 97

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