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

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Basic information

Entry
Database: PDB / ID: 5klc
TitleStructure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome
ComponentsCarbohydrate binding module E1
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / metagenomics / cellulose / biofuels
Function / homologyCarbohydrate binding module E1
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.746 Å
AuthorsLiberato, M.V. / Campos, B.M. / Zeri, A.C.M. / Squina, F.M.
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 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding module E1


Theoretical massNumber of molelcules
Total (without water)10,0121
Polymers10,0121
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.391, 26.514, 99.294
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-589-

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 1.94 Å3/Da / Density % sol: 36.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2 M ammonium sulfate, 0.2 M lithium sulfate and 0.1 M CAPS, pH 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.74→27.62 Å / Num. obs: 7638 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.74-1.785.50.9721.9181
9.06-27.625.90.03429.8197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.2data scaling
PHASER2.5.7phasing
PHENIX1.10.1refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLF

5klf


Resolution: 1.746→26.922 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.24
RfactorNum. reflection% reflection
Rfree0.2073 412 5.4 %
Rwork0.1539 --
obs0.1566 7635 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.25 Å2 / Biso mean: 17.0854 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 1.746→26.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 0 116 792
Biso mean---29.64 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006690
X-RAY DIFFRACTIONf_angle_d0.815937
X-RAY DIFFRACTIONf_chiral_restr0.059103
X-RAY DIFFRACTIONf_plane_restr0.004121
X-RAY DIFFRACTIONf_dihedral_angle_d7.846393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7464-1.99910.27941340.18592336247098
1.9991-2.51830.1841730.147923732546100
2.5183-26.92480.2011050.147825142619100
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)
11.4162-0.10350.38912.0687-0.78931.982-0.03150.163-0.01190.1210.03080.0622-0.06970.00950.00480.1421-0.01720.00570.1415-0.02140.1044-5.3022-7.6245-20.3094
22.6653-2.10641.79924.1887-0.13771.86420.03070.2852-0.2466-0.08760.00750.07760.11660.20120.06490.0990.02360.00220.14180.02760.13522.0824-2.7958-18.3776
32.70971.80090.06056.674-2.71444.57930.0490.0388-0.0823-0.25330.00670.1070.4681-0.0914-0.06410.1246-0.0151-0.01650.1085-0.01920.1381-7.6913-10.6979-16.083
43.52880.18370.441.6429-0.73282.89110.106-0.1898-0.06910.0377-0.0350.21170.3208-0.1464-0.0750.1639-0.02870.00520.11760.0150.1096-6.0013-10.5825-6.2028
53.32250.08340.81274.3214-1.41172.83740.03440.1990.03690.0044-0.2403-0.181-0.13810.16810.17110.1418-0.0345-0.01920.14460.020.11986.9348-1.3257-7.2491
62.78530.17590.60352.5124-0.94512.3953-0.0357-0.0620.1280.13160.00850.0569-0.1555-0.10010.06270.11320.0017-0.00170.0996-0.00870.1055-5.3893-1.374-7.91
74.62762.24981.05513.0932-0.4251.8732-0.0501-0.11490.0757-0.05530.11520.26860.1233-0.12-0.0890.09460.01830.00870.126-0.00940.1209-9.4688-5.0587-13.6178
84.13794.9952-3.02068.3783-5.91755.2783-0.05230.1146-0.08380.00170.015-0.01510.14340.21970.01460.09290.0204-0.00030.10560.01230.14791.7227-6.6631-10.1613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 335 through 352 )A335 - 352
2X-RAY DIFFRACTION2chain 'A' and (resid 353 through 359 )A353 - 359
3X-RAY DIFFRACTION3chain 'A' and (resid 360 through 365 )A360 - 365
4X-RAY DIFFRACTION4chain 'A' and (resid 366 through 374 )A366 - 374
5X-RAY DIFFRACTION5chain 'A' and (resid 375 through 379 )A375 - 379
6X-RAY DIFFRACTION6chain 'A' and (resid 380 through 401 )A380 - 401
7X-RAY DIFFRACTION7chain 'A' and (resid 402 through 416 )A402 - 416
8X-RAY DIFFRACTION8chain 'A' and (resid 417 through 427 )A417 - 427

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