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- PDB-6wb5: Microbiome-derived Acarbose Kinase Mak1 as a Complex with Acarbos... -

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Basic information

Entry
Database: PDB / ID: 6wb5
TitleMicrobiome-derived Acarbose Kinase Mak1 as a Complex with Acarbose and AMP-PNP
ComponentsAcarbose Kinase Mak1
KeywordsTRANSFERASE / CARBOHYDRATE KINASE / ACARBOSE / NUCLEOTIDE BINDING / ATP BINDING / METAL ION BINDING / RIBOKINASE ACTIVITY / COMPLEX
Function / homologyRibokinase / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta / alpha-acarbose / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / :
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å
AuthorsJeffrey, P.D. / Balaich, J.N. / Estrella, M.A. / Donia, M.S.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
CitationJournal: Nature / Year: 2021
Title: The human microbiome encodes resistance to the antidiabetic drug acarbose.
Authors: Balaich, J. / Estrella, M. / Wu, G. / Jeffrey, P.D. / Biswas, A. / Zhao, L. / Korennykh, A. / Donia, M.S.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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: Acarbose Kinase Mak1
B: Acarbose Kinase Mak1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8008
Polymers68,3872
Non-polymers2,4136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-67 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.551, 86.551, 164.334
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 402
211chain BB-6 - 402

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Components

#1: Protein Acarbose Kinase Mak1


Mass: 34193.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET28a / Production host: Escherichia coli (E. coli)
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.25 M Ammonium Dihydrogen Phosphate, 0.1M Tris-HCl pH 8.3, 10 mM MnCl2, 6 mM AMP-PNP, 50 mM Acarbose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 3.1→28.33 Å / Num. obs: 12632 / % possible obs: 99.7 % / Redundancy: 14.4 % / Biso Wilson estimate: 66.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.046 / Rrim(I) all: 0.177 / Net I/σ(I): 16 / Num. measured all: 181665
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
3.1-3.1814.11.085125698930.8210.2951.1262.797.4
13.87-28.3313.90.04119451400.9990.0120.04251.689.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WB4

6wb4


Resolution: 3.102→28.33 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2491 688 5.47 %
Rwork0.163 --
obs0.1679 12583 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 282.14 Å2 / Biso mean: 61.6553 Å2 / Biso min: 15.04 Å2
Refinement stepCycle: final / Resolution: 3.102→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 152 0 4708
Biso mean--73.97 --
Num. residues----605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074830
X-RAY DIFFRACTIONf_angle_d1.0066593
X-RAY DIFFRACTIONf_chiral_restr0.038764
X-RAY DIFFRACTIONf_plane_restr0.005839
X-RAY DIFFRACTIONf_dihedral_angle_d15.3791717
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2564X-RAY DIFFRACTION13.768TORSIONAL
12B2564X-RAY DIFFRACTION13.768TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1023-3.34150.33541320.2278234999
3.3415-3.67710.29631390.18552375100
3.6771-4.20770.25131360.15692382100
4.2077-5.29560.21591430.13942381100
5.2956-28.330.22511380.15562408100
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)
10.0213-0.0447-0.0090.01650.02040.00680.1287-0.0649-0.04630.08960.0221-0.0155-0.00110.1354-00.3591-0.07860.01820.3718-0.06810.302618.612537.172416.9378
2-0.0042-0.0150.01490.2045-0.0560.14970.1106-0.1320.0560.2564-0.13060.31210.0809-0.2229-0.02790.1460.0738-0.1130.24830.15930.146914.561429.386714.9304
30.14680.01920.11380.1076-0.06580.127-0.02940.1785-0.2769-0.12710.1651-0.3762-0.18870.07320.08020.06960.1721-0.22280.13280.03080.305124.933131.07972.5118
40.04440.08090.0090.1566-0.02730.11380.16340.0773-0.0056-0.0126-0.0728-0.0162-0.283-0.175500.28160.06510.00110.3467-0.01520.26715.105745.4815-0.4838
50.002-0.0391-0.0160.0385-0.04670.002-0.03330.0445-0.0599-0.11420.05820.07670.00960.0799-00.4336-0.0627-0.02580.5480.07560.370221.526331.821634.8851
60.1534-0.124-0.13230.2212-0.06070.3119-0.05520.02080.1119-0.160.26270.36490.0713-0.19660.23280.2322-0.0081-0.05810.36120.13460.291316.098535.403846.8988
70.00330.01160.04320.09-0.05290.06710.1426-0.0604-0.0616-0.1692-0.0882-0.0731-0.22050.158300.3257-0.02190.09910.30860.03060.326132.724441.025356.3256
80.0240.0216-0.01130.02070.01640.01770.2354-0.1104-0.1275-0.194-0.0215-0.14360.28530.23070.00020.41870.1048-0.00990.34090.03250.288232.836626.998852.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A1 - 30
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 101 )A31 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 190 )A102 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 299 )A191 - 299
5X-RAY DIFFRACTION5chain 'B' and (resid -6 through 42 )B-6 - 42
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 190 )B43 - 190
7X-RAY DIFFRACTION7chain 'B' and (resid 191 through 244 )B191 - 244
8X-RAY DIFFRACTION8chain 'B' and (resid 245 through 299 )B245 - 299

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