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Basic information

Entry
Database: PDB / ID: 3o7o
TitleUse of synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima
ComponentsEndoglucanase
KeywordsHYDROLASE / Macromolecular crystallization / Synthetic symmetrization / Protein design / Oligomer / lattice contact / Disulfide bond
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Endoglucanase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsForse, G.J. / Ram, N. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2011
Title: Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.
Authors: Forse, G.J. / Ram, N. / Banatao, D.R. / Cascio, D. / Sawaya, M.R. / Klock, H.E. / Lesley, S.A. / Yeates, T.O.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9169
Polymers61,3572
Non-polymers5597
Water1,29772
1


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


Theoretical massNumber of molelcules
Total (without water)30,9184
Polymers30,6791
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9985
Polymers30,6791
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.028, 114.028, 98.818
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Endoglucanase


Mass: 30678.537 Da / Num. of mol.: 2 / Mutation: D188C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1524, TM_1524 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9S5X8
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0259.31
2
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2 M NaBr, 0.1 M TRIS-HCl pH 8.3, 42% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9794
SYNCHROTRONAPS 24-ID-E20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 25, 2010
ADSC QUANTUM 3152CCDApr 26, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si (111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97911
ReflectionNumber: 101738 / Rmerge(I) obs: 0.095 / D res high: 2.3 Å / Num. obs: 55558 / % possible obs: 86.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.32.36397483.112.082
2.362.43401486.411.744
2.432.5391786.811.287
2.52.57377986.511.049
2.572.66371386.610.739
2.662.75356286.710.507
2.752.86344987.110.394
2.862.97330786.910.299
2.973.1321387.210.203
3.13.26303787.210.146
3.263.43291187.310.102
3.433.64274786.910.078
3.643.89258587.610.062
3.894.2238986.710.054
4.24.6219986.710.045
4.65.15197486.210.043
5.155.9417168510.044
5.947.28146385.610.042
7.2810.29109782.910.036
10.2969.8515126910.034
ReflectionResolution: 2.4→98.75 Å / Num. obs: 27835 / % possible obs: 97 % / Observed criterion σ(I): -2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 85.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
DMphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
Adxvdata processing
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.41→20.18 Å / Cor.coef. Fo:Fc: 0.9031 / Cor.coef. Fo:Fc free: 0.8683 / Occupancy max: 1 / Occupancy min: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2157 1404 5.09 %RANDOM
Rwork0.1756 ---
obs0.1776 27569 --
Displacement parametersBiso max: 180.77 Å2 / Biso mean: 46.3234 Å2 / Biso min: 22.35 Å2
Baniso -1Baniso -2Baniso -3
1--10.4833 Å20 Å20 Å2
2---10.4833 Å20 Å2
3---20.9667 Å2
Refine analyzeLuzzati coordinate error obs: 0.319 Å
Refinement stepCycle: LAST / Resolution: 2.41→20.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 7 72 4395
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d14822
X-RAY DIFFRACTIONt_trig_c_planes1062
X-RAY DIFFRACTIONt_gen_planes6375
X-RAY DIFFRACTIONt_it446420
X-RAY DIFFRACTIONt_nbd15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5375
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact48154
X-RAY DIFFRACTIONt_bond_d446420.009
X-RAY DIFFRACTIONt_angle_deg606221.1
X-RAY DIFFRACTIONt_omega_torsion3.65
X-RAY DIFFRACTIONt_other_torsion19.34
LS refinement shellResolution: 2.41→2.5 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3515 119 4.13 %
Rwork0.2889 2763 -
all0.2913 2882 -
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)
12.91010.09181.08361.5607-0.26622.36880.0622-0.24680.490.0804-0.1306-0.0147-0.28670.00060.0684-0.0927-0.0532-0.0346-0.1221-0.0219-0.049460.134668.441568.7225
21.54450.1723-0.0961.7422-0.57782.58660.01190.0788-0.0157-0.04030.0357-0.0032-0.2158-0.2612-0.0476-0.0955-0.06610.0547-0.00670.0281-0.126287.856448.882343.997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 264
2X-RAY DIFFRACTION2{ B|* }B1 - 262

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