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- PDB-7ctl: Crystal structure of NADH bound holo form of alpha-glucuronidase ... -

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Basic information

Entry
Database: PDB / ID: 7ctl
TitleCrystal structure of NADH bound holo form of alpha-glucuronidase (TM0752) from Thermotoga maritima at 1.97 Angstrom resolution
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5612
Polymers56,8961
Non-polymers6651
Water5,459303
1
A: Alpha-glucosidase, putative
hetero molecules

A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1234
Polymers113,7922
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area5250 Å2
ΔGint-25 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.720, 81.280, 89.000
Angle α, β, γ (deg.)90.000, 103.030, 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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
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, 7 mM NADH, 7 mM DTT

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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: Aug 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→29.65 Å / Num. obs: 35756 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.059 / Rrim(I) all: 0.153 / Net I/σ(I): 9.6 / Num. measured all: 233223 / Scaling rejects: 41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.97-2.026.71.2721.525700.5960.5331.382100
9.03-29.656.80.03532.53790.9980.0140.03897.2

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
Aimless0.5.17data scaling
PHENIX1.11.1refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KCX

6kcx


Resolution: 1.97→29.65 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 1783 4.99 %random
Rwork0.1763 33960 --
obs0.1785 35743 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 38.0452 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 1.97→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3774 0 71 303 4148
Biso mean--43.65 36.34 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073935
X-RAY DIFFRACTIONf_angle_d0.8045357
X-RAY DIFFRACTIONf_chiral_restr0.049572
X-RAY DIFFRACTIONf_plane_restr0.005686
X-RAY DIFFRACTIONf_dihedral_angle_d11.2012332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.97-2.02330.31731240.28272672
2.0233-2.08280.30671170.24492588
2.0828-2.150.24521350.23132594
2.15-2.22680.26871530.22512563
2.2268-2.31590.29331300.22932618
2.3159-2.42130.2521250.19212614
2.4213-2.54890.2221430.18222593
2.5489-2.70850.23411410.17812620
2.7085-2.91740.23321280.1922588
2.9174-3.21070.25361380.18532628
3.2107-3.67460.21031610.15452588
3.6746-4.62680.16761430.12732632
4.6268-29.650.18431450.15012662
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)
11.2125-0.06930.37961.4319-0.0941.43960.02240.5450.1078-0.7232-0.01970.1588-0.3075-0.02860.01280.62270.0273-0.00930.44940.03290.22241.4964.534389.1574
20.8754-0.21340.12791.76950.01561.17070.03050.0887-0.1055-0.3221-0.01460.19890.0207-0.0895-0.01760.1915-0.0021-0.0450.163-0.02270.1735-3.5369-4.8263114.028
30.0925-0.0195-0.16850.30920.22931.0373-0.11240.3799-0.13-0.45690.1320.2840.3619-0.1541-0.04140.7393-0.0506-0.1230.6191-0.09550.4496-6.5643-9.345290.4665
40.879-0.12530.09181.1768-0.13891.61610.11260.0940.05-0.3029-0.0733-0.0619-0.16120.0292-0.03260.21740.00370.03320.1725-0.00960.19746.28880.8884117.2164
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 297 )A83 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 345 )A298 - 345
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 468 )A346 - 468

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