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- PDB-7br4: Structure of deletion mutant of alpha-glucuronidase (TM0752) from... -

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Basic information

Entry
Database: PDB / ID: 7br4
TitleStructure of deletion mutant of alpha-glucuronidase (TM0752) from Thermotoga maritima
ComponentsAlpha-glucosidase, putative
KeywordsHYDROLASE / hydrolase-oxidoreductase / alpha-glucuronidase activity / carbohydrate metabolism / NAD-binding Rossmann-fold / LDH C-terminal domain-like
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
: / : / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsManoj, N. / Mohapatra, S.B.
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2021
Title: A conserved pi-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4.
Authors: Mohapatra, S.B. / Manoj, N.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4693
Polymers56,7491
Non-polymers7202
Water5,386299
1
A: Alpha-glucosidase, putative
hetero molecules

A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9386
Polymers113,4972
Non-polymers1,4414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5100 Å2
ΔGint-39 kcal/mol
Surface area34760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.350, 80.150, 88.860
Angle α, β, γ (deg.)90.000, 102.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-895-

HOH

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Components

#1: Protein Alpha-glucosidase, putative


Mass: 56748.676 Da / Num. of mol.: 1 / Mutation: Deletion Phe407
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_0752 / Plasmid: pMH2T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9WZL1
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole pH 6.0, 2-propanol
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: Jul 19, 2017
RadiationMonochromator: Double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→43.45 Å / Num. obs: 36415 / % possible obs: 96.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.39 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.061 / Rrim(I) all: 0.132 / Net I/σ(I): 6.2 / Num. measured all: 156648 / Scaling rejects: 179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-24.20.53225860.7590.2830.60397.9
8.94-43.454.40.0434080.9970.0230.04998.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.97 Å43.45 Å
Translation5.97 Å43.45 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.4data scaling
PHASER2.7.16phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJT

1vjt


Resolution: 1.95→29.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1813 4.98 %random
Rwork0.1943 ---
obs0.1962 36374 96.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.31 Å2 / Biso mean: 27.2354 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: final / Resolution: 1.95→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3768 0 57 299 4124
Biso mean--23.69 28.6 -
Num. residues----468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043906
X-RAY DIFFRACTIONf_angle_d0.6635317
X-RAY DIFFRACTIONf_chiral_restr0.045569
X-RAY DIFFRACTIONf_plane_restr0.004683
X-RAY DIFFRACTIONf_dihedral_angle_d11.1072307
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-2.00270.34121300.2621268298
2.0027-2.06170.24721320.2338269597
2.0617-2.12820.25961240.2142264496
2.1282-2.20420.21041420.2025262795
2.2042-2.29240.28841470.2466260895
2.2924-2.39670.29971320.254256694
2.3967-2.5230.31121190.2607256893
2.523-2.6810.26261510.2161256494
2.681-2.88780.25231230.2003261995
2.8878-3.17810.23851450.1974266997
3.1781-3.63730.2311610.18062743100
3.6373-4.57990.17291520.13662765100
4.5799-29.460.18361550.15312811100
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)
11.7977-0.23540.89111.830.37852.70980.02320.2796-0.0033-0.3425-0.05430.0972-0.0315-0.18440.02940.2588-0.00030.0120.27220.00020.131823.0415.08022.5082
20.95740.38740.19882.3585-1.36371.44210.03360.0129-0.0806-0.141-0.01430.01290.04730.1496-0.03190.17110.04470.02220.1684-0.0220.144432.2203-8.708621.6199
32.44710.0609-0.72351.1916-0.13760.8621-0.12470.04430.0495-0.14380.09490.1627-0.032-0.11540.02330.16290.0196-0.03520.11020.00220.108614.65195.951726.7115
40.6867-0.26250.12822.00380.34741.62580.03570.0223-0.1683-0.0227-0.01810.24190.1366-0.216-0.02480.1103-0.03520.01080.14020.00870.18698.9439-10.694633.5558
50.749-0.3501-0.14631.3625-2.50055.5064-0.32120.1449-0.0235-0.32580.0857-0.0503-0.1634-0.13730.24280.4339-0.0463-0.0470.2898-0.09950.245619.5426-14.15116.2016
60.8532-0.2414-0.42132.02930.86323.2688-0.02610.3307-0.1625-0.287-0.09860.3210.0023-0.47970.12790.19290.0252-0.0230.3018-0.03560.221313.4286.05119.866
70.7580.4687-0.66730.41660.00991.96770.0148-0.07250.02550.00360.03360.0626-0.17870.0089-0.04660.13520.01550.00180.1103-0.0090.124222.75228.453234.2031
80.77070.47410.65692.0357-0.70711.8848-0.01930.028-0.0809-0.1125-0.0258-0.30660.21150.05260.04810.14260.06740.01380.1819-0.01180.194240.4621-13.482631.3118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 82 )A0 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 149 )A83 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 224 )A150 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 297 )A225 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 322 )A298 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 366 )A323 - 366
7X-RAY DIFFRACTION7chain 'A' and (resid 367 through 424 )A367 - 424
8X-RAY DIFFRACTION8chain 'A' and (resid 425 through 468 )A425 - 468

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