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- PDB-5e9o: Spirochaeta thermophila X module - CBM64 - mutant G504A -

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Basic information

Entry
Database: PDB / ID: 5e9o
TitleSpirochaeta thermophila X module - CBM64 - mutant G504A
ComponentsCellulase, glycosyl hydrolase family 5, TPS linker, domain X
KeywordsHYDROLASE / Carbohydrate-binding module 64 / CBM64 / Cellulose and Xylan binding / Type A CBM / Jelly roll
Function / homology
Function and homology information


cellulase / metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Carbohydrate-binding module 64 / Carbohydrate-binding module 64 / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-I3C / cellulase
Similarity search - Component
Biological speciesSpirochaeta thermophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Proteins / Year: 2016
Title: Structural basis for cellulose binding by the type A carbohydrate-binding module 64 of Spirochaeta thermophila.
Authors: Schiefner, A. / Angelov, A. / Liebl, W. / Skerra, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
B: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
C: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
D: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9539
Polymers40,1594
Non-polymers2,7945
Water3,279182
1
A: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X


Theoretical massNumber of molelcules
Total (without water)10,0401
Polymers10,0401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5992
Polymers10,0401
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1573
Polymers10,0401
Non-polymers1,1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cellulase, glycosyl hydrolase family 5, TPS linker, domain X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1573
Polymers10,0401
Non-polymers1,1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.929, 144.929, 144.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Cellulase, glycosyl hydrolase family 5, TPS linker, domain X


Mass: 10039.781 Da / Num. of mol.: 4 / Fragment: UNP residues 456-541 / Mutation: G504A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spirochaeta thermophila (bacteria) / Gene: STHERM_c20620 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0RQU0
#2: Chemical
ChemComp-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1.6 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.8 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 57408 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 33.079 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.092 / Χ2: 1.653 / Net I/σ(I): 21.7 / Num. measured all: 612788
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.1-2.27.10.8430.5823.2352943750475040.629100
2.2-2.30.9350.4725.2367182621762170.496100
2.3-2.50.970.3337.52107284969796970.349100
2.5-30.9950.14716.3516110714318143180.154100
3-3.50.9990.06534.1182740726772670.068100
3.5-40.9990.04546.0546939411241120.048100
4-60.9990.0452.5166771584458440.041100
6-810.03852.2316259140814080.04100
8-100.9990.03458.6157695085080.036100
100.9990.03565.257945475330.03797.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SHELXphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.1→34.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.2009 / WRfactor Rwork: 0.1627 / FOM work R set: 0.8702 / SU B: 7.373 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1698 / SU Rfree: 0.1554 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 1507 5.1 %RANDOM
Rwork0.1787 ---
obs0.1807 28110 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.16 Å2 / Biso mean: 30.607 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 80 183 3103
Biso mean--41.33 32.42 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023032
X-RAY DIFFRACTIONr_bond_other_d0.0010.022454
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9154176
X-RAY DIFFRACTIONr_angle_other_deg0.81435631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2845336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30824.634164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74115392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.286154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 144 -
Rwork0.236 2005 -
all-2149 -
obs--100 %
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)
11.7720.56560.74584.95174.02196.92350.1211-0.2685-0.2070.2817-0.2140.02180.3095-0.75360.09290.0238-0.0328-0.00810.12580.01230.029255.460433.5036137.7609
23.5671-0.252-3.98081.02060.18545.52610.30320.31710.0033-0.171-0.23150.0688-0.2679-0.4857-0.07170.07840.0874-0.01930.1426-0.01330.009842.603152.5179142.5536
33.2315-2.3384-0.26375.17540.07981.3679-0.1686-0.2602-0.4760.12180.05260.13150.1956-0.00320.1160.05540.040.07670.06850.10330.168246.068933.2893163.8451
48.31630.2465-1.330.43970.27283.01820.2884-0.59510.2855-0.0197-0.01210.2929-0.415-0.1476-0.27640.136-0.01470.0440.07630.02950.269870.757155.3812156.4281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A457 - 541
2X-RAY DIFFRACTION2B457 - 541
3X-RAY DIFFRACTION3C457 - 541
4X-RAY DIFFRACTION4D457 - 541

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