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- PDB-7brf: Structure of NADH complex of Thermotoga maritima alpha-glucuronid... -

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Basic information

Entry
Database: PDB / ID: 7brf
TitleStructure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution
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 / Resolution: 2.15 Å
AuthorsManoj, N. / Mohapatra, S.B.
CitationJournal: To Be Published
Title: Structure of NADH complex of Thermotoga maritima alpha-glucuronidase at 2.15 Angstrom resolution
Authors: Manoj, N. / Mohapatra, S.B.
History
DepositionMar 28, 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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5772
Polymers56,9121
Non-polymers6651
Water3,783210
1
A: Alpha-glucosidase, putative
hetero molecules

A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1554
Polymers113,8242
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5250 Å2
ΔGint-27 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.330, 81.060, 88.760
Angle α, β, γ (deg.)90.000, 103.020, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-glucosidase, putative


Mass: 56911.852 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) / Strain (production host): BL21(DE3) / Variant (production host): Codon Plus 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.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 45.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 12-18% PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole 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: Feb 20, 2014
RadiationMonochromator: Double Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→36.833 Å / Num. obs: 27625 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.36 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.073 / Rrim(I) all: 0.191 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.15-2.226.40.991.923880.5940.4241.079100
8.86-36.836.50.04924.64130.9980.0210.05398.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
MOSFLMdata reduction
Aimless0.5.9data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJT

1vjt


Resolution: 2.15→36.833 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.13 / Details: Hydrogen atoms are included in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 1416 5.13 %Random
Rwork0.178 ---
obs0.1799 27619 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.04 Å2 / Biso mean: 40.1634 Å2 / Biso min: 15.38 Å2
Refinement stepCycle: final / Resolution: 2.15→36.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3763 0 71 210 4044
Biso mean--65.03 33.95 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023911
X-RAY DIFFRACTIONf_angle_d0.5285325
X-RAY DIFFRACTIONf_chiral_restr0.042570
X-RAY DIFFRACTIONf_plane_restr0.003682
X-RAY DIFFRACTIONf_dihedral_angle_d11.3132308
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.15-2.22680.33041630.2722581
2.2268-2.3160.28851250.24712631
2.316-2.42140.25511310.22232604
2.4214-2.5490.22911370.2052615
2.549-2.70870.25351420.19422619
2.7087-2.91770.25461280.20052614
2.9177-3.21120.21311400.19332628
3.2112-3.67550.20121610.16492600
3.6755-4.62930.16271440.12832636
4.6293-36.830.18411450.15072675
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)
11.4895-0.010.30011.36180.06781.73590.04330.4603-0.0157-0.7095-0.07620.1192-0.2037-0.0644-0.03620.60150.0261-0.01060.42120.00290.227521.98194.95922.268
20.93880.1101-0.03641.2896-0.0940.9326-0.00910.1126-0.0972-0.28310.02240.14390.039-0.0859-0.02310.2155-0.0071-0.0340.209-0.02480.214616.8391-4.55527.1197
30.3030.0285-0.18011.5207-1.92952.5206-0.22390.269-0.128-0.6793-0.02510.11590.2911-0.13160.00530.7352-0.0764-0.06860.438-0.12890.394418.2617-14.40675.5431
40.7156-0.0593-0.17690.964-0.15671.59760.03590.0884-0.0051-0.27880.02080.02-0.0993-0.0707-0.03590.2265-0.01250.01420.2027-0.01560.229124.10630.623926.2126
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 322 )A298 - 322
4X-RAY DIFFRACTION4chain 'A' and (resid 323 through 468 )A323 - 468

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