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- PDB-7efz: Structure of Thermotoga maritima GH5 endoglucanase TM1752 in comp... -

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Basic information

Entry
Database: PDB / ID: 7efz
TitleStructure of Thermotoga maritima GH5 endoglucanase TM1752 in complex with TRIS
ComponentsEndoglucanase
KeywordsHYDROLASE / TIM barrel / Glycoside hydrolase / Endoglucanase
Function / homologyglucan exo-1,3-beta-glucosidase activity / : / glucan catabolic process / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulose catabolic process / Glycoside hydrolase superfamily / ISOPROPYL ALCOHOL / Endoglucanase
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsManoj, N. / Garg, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR-13040/FNS/20/416/2009 India
CitationJournal: To Be Published
Title: Structure of Thermotoga maritima GH5 endoglucanase TM1752 in complex with TRIS
Authors: Manoj, N. / Garg, P.
History
DepositionMar 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)82,0567
Polymers81,6312
Non-polymers4255
Water12,286682
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9983
Polymers40,8151
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0584
Polymers40,8151
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 61.610, 201.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase


Mass: 40815.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1752 / Plasmid: pMH4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9X274
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium citrate tribasic dihydrate (pH 5.8-6.2), 8-14% (v/v) isopropanol, 8-16% (w/v) PEG 4000
PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→40.34 Å / Num. obs: 83492 / % possible obs: 97 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.03 / Rrim(I) all: 0.083 / Net I/σ(I): 13 / Num. measured all: 553735 / Scaling rejects: 3549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.724.50.4241559334920.8290.2190.4792.578.5
8.94-40.3412.40.04585586890.9990.0130.04732.699

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
MOSFLMdata reduction
Aimless0.5.27data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJZ

1vjz


Resolution: 1.69→39.019 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 2511 3.01 %
Rwork0.1551 80886 -
obs0.156 83397 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.97 Å2 / Biso mean: 16.9021 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: final / Resolution: 1.69→39.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 74 682 6154
Biso mean--28.93 24.21 -
Num. residues----648
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.69-1.72250.33931030.3016355878
1.7225-1.75770.35741210.2739392985
1.7577-1.79590.26141160.2369416291
1.7959-1.83770.23441500.2052430894
1.8377-1.88360.20321350.1752443497
1.8836-1.93450.22371320.1761451998
1.9345-1.99150.2081540.15444564100
1.9915-2.05570.17351240.14814625100
2.0557-2.12920.20421620.14294565100
2.1292-2.21450.18831440.14234631100
2.2145-2.31520.18161430.14234602100
2.3152-2.43730.19711440.14374639100
2.4373-2.58990.15931570.14024606100
2.5899-2.78990.17381410.14964679100
2.7899-3.07050.18781460.14824658100
3.0705-3.51460.17821340.14974701100
3.5146-4.4270.14731330.13284779100
4.427-39.0190.14921720.154927100
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)
12.0642-0.0340.86311.617-1.26572.4425-0.0681-0.05460.03970.05670.0191-0.1755-0.06820.12310.03490.08330.0062-0.00420.0562-0.03480.074113.302410.234518.8381
20.64180.0858-0.06660.4734-0.44151.96680.0275-0.00070.05080.020.011-0.03410.03420.1754-0.02680.0958-0.0148-0.01360.0884-0.01640.109614.410910.344323.8383
30.99740.5650.05441.8407-0.52620.8415-0.0267-0.01160.040.11570.0115-0.1983-0.12010.11780.01540.1186-0.0289-0.00710.1002-0.01480.121115.874415.644725.5809
41.27290.111-0.010.844-0.10451.2530.0192-0.1406-0.04210.08520.0006-0.01390.065-0.055-0.0230.0899-0.0066-0.00350.0650.00110.06283.87045.011832.3743
51.31211.11420.70892.01210.86151.72670.0963-0.19020.1240.2499-0.06510.1259-0.0379-0.1723-0.02710.12670.01540.03230.0967-0.01360.0992-2.360911.555833.648
60.79970.62070.82451.94180.48390.9403-0.0433-0.08880.05650.1032-0.00470.1444-0.0673-0.12810.04420.08580.0110.0010.0850.01350.1016-4.96868.209419.6534
71.83610.1350.36161.0759-0.02311.63470.08990.0541-0.4065-0.03620.00940.02610.2844-0.1399-0.09430.1268-0.0211-0.00080.1022-0.01820.1643-2.442-5.28786.4458
81.581-0.3634-0.16471.48830.3191.76370.0177-0.02170.05540.06840.05540.0569-0.1357-0.172-0.0740.08710.01230.00770.08190.01380.0957-6.00499.965412.9518
92.9758-1.7233-1.0342.21530.58261.4750.07740.15130.0157-0.128-0.0307-0.0355-0.0375-0.1497-0.05740.06860.0023-0.00830.1119-0.00540.0821-1.709710.36872.8323
101.00980.1484-0.38380.59560.13730.9471-0.02460.10720.0031-0.08630.0236-0.007-0.0130.06390.00050.0807-0.0135-00.1134-0.00450.087711.939610.73174.4754
110.89960.2982-0.27220.8535-0.34851.4226-0.00350.0217-0.0468-0.08240.00540.06930.1282-0.02840.00980.0773-0.0083-0.02640.061-0.00730.0828-24.1151-27.385823.6511
122.69321.18340.79991.16280.48561.5384-0.00530.28480.1625-0.15530.07150.1892-0.058-0.053-0.06050.10640.0099-0.03470.10440.03040.1284-27.2135-15.235116.7325
131.54350.1840.52651.21870.13331.4586-0.0094-0.04320.09170.0385-0.0373-0.0272-0.17590.01640.06710.1027-0.0150.01240.0704-0.00210.0962-19.5469-10.467537.4162
140.79420.02230.25431.2953-0.21871.15840.003-0.14140.00820.1358-0.01780.0126-0.035-0.11050.0130.0794-0.01350.00210.1140.0030.0731-25.0677-23.511544.8837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 26 )A6 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 60 )A27 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 87 )A61 - 87
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 149 )A88 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 181 )A150 - 181
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 206 )A182 - 206
7X-RAY DIFFRACTION7chain 'A' and (resid 207 through 234 )A207 - 234
8X-RAY DIFFRACTION8chain 'A' and (resid 235 through 267 )A235 - 267
9X-RAY DIFFRACTION9chain 'A' and (resid 268 through 285 )A268 - 285
10X-RAY DIFFRACTION10chain 'A' and (resid 286 through 329 )A286 - 329
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 149 )B6 - 149
12X-RAY DIFFRACTION12chain 'B' and (resid 150 through 181 )B150 - 181
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 251 )B182 - 251
14X-RAY DIFFRACTION14chain 'B' and (resid 252 through 329 )B252 - 329

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