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- PDB-7ctd: Crystal structure of apo form of alpha-glucuronidase (TM0752) fro... -

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Basic information

Entry
Database: PDB / ID: 7ctd
TitleCrystal structure of apo form of alpha-glucuronidase (TM0752) from Thermotoga maritima
ComponentsAlpha-glucosidase, putative
KeywordsHYDROLASE / Glycosyl hydrolase family 4 / NAD(P)-binding Rossmann-fold domain / LDH C-terminal domain-like / hydrolase activity / alpha-glucuronidase
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
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
Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsManoj, N. / Mohapatra, B.S.
CitationJournal: Biochem.J. / Year: 2021
Title: Structural basis of catalysis and substrate recognition by the NAD(H)-dependent alpha-d-glucuronidase from the glycoside hydrolase family 4.
Authors: Mohapatra, S.B. / Manoj, N.
History
DepositionAug 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.identifier_ORCID / _citation_author.name
Revision 1.2Nov 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: Alpha-glucosidase, putative


Theoretical massNumber of molelcules
Total (without water)56,8961
Polymers56,8961
Non-polymers00
Water3,369187
1
A: Alpha-glucosidase, putative

A: Alpha-glucosidase, putative


Theoretical massNumber of molelcules
Total (without water)113,7922
Polymers113,7922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2990 Å2
ΔGint-15 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.690, 80.950, 88.380
Angle α, β, γ (deg.)90.000, 103.440, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-glucosidase, putative


Mass: 56895.852 Da / Num. of mol.: 1
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) / Variant (production host): RIL / References: UniProt: Q9WZL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 14 % PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole with pH 5.8, 2-propanol

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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: Jun 2, 2014
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→29.466 Å / Num. obs: 27091 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.07 / Rrim(I) all: 0.183 / Rsym value: 0.169 / Net I/av σ(I): 4.3 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.15-2.276.60.8990.939740.5810.3760.9770.899100
2.27-2.46.60.7281.137100.3040.790.728100
2.4-2.576.70.5661.434970.2350.6140.56699.9
2.57-2.786.70.4171.832530.1720.4530.41799
2.78-3.046.70.3052.529830.1260.3310.30598.7
3.04-3.46.70.1654.527510.0680.1790.16599.8
3.4-3.936.80.1056.823850.0430.1140.105100
3.93-4.816.80.0719.320620.0290.0770.071100
4.81-6.86.80.05413.116030.0220.0580.054100
6.8-30.36.70.02928.88730.9990.0120.0310.02998.8

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Processing

Software
NameVersionClassification
PHENIX1.16-3549refinement
MOSFLM7.1data reduction
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KCX

6kcx


Resolution: 2.15→29.466 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1387 5.12 %
Rwork0.1785 25700 -
obs0.1808 27087 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.01 Å2 / Biso mean: 43.7105 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 2.15→29.466 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 0 187 3956
Biso mean---33.06 -
Num. residues----469
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.22680.29231480.28322527100
2.2268-2.31590.31571270.25172578100
2.3159-2.42130.26831240.24692583100
2.4213-2.54890.26671410.21532569100
2.5489-2.70850.26311380.2046256499
2.7085-2.91740.23611250.202254799
2.9174-3.21070.2331430.1915255099
3.2107-3.67460.22061570.1532557100
3.6746-4.62670.18911410.12972595100
4.6267-29.4660.17811430.15032630100
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)
12.48340.12620.56142.29890.19952.62760.02460.62520.0555-0.8161-0.07070.2369-0.37110.04730.0450.54560.0684-0.01210.42710.02250.21531.23784.644488.0601
20.67540.24460.39851.8815-0.87341.56840.00040.2446-0.2405-0.6933-0.0754-0.17910.27020.22270.07460.43160.05080.1050.2788-0.04850.34099.5194-9.1385107.2823
32.7416-1.4477-0.85420.83560.22362.14620.180.1986-0.0338-0.3374-0.08630.1008-0.0956-0.0688-0.07030.3641-0.00840.0040.2032-0.02170.26740.44695.4904108.3685
41.4833-0.25420.45072.620.07571.3605-0.02740.0084-0.2641-0.24460.06120.55290.1362-0.3225-0.02050.1921-0.0365-0.00310.24860.00130.3006-15.0536-5.9469118.3946
50.10640.0259-0.43591.0549-2.66988.016-0.21970.1886-0.053-0.8124-0.01170.25020.938-0.64540.18660.7271-0.0201-0.08740.4442-0.14910.4453-3.2265-14.27791.0012
60.6852-0.03910.09751.0515-0.31492.26370.06170.1129-0.0543-0.2254-0.03480.0886-0.1067-0.0806-0.03320.2629-0.01360.05140.1877-0.03070.25623.28610.451112.1126
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 193 )A150 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 297 )A194 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 322 )A298 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 468 )A323 - 468

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