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- PDB-6wb4: Microbiome-derived Acarbose Kinase Mak1 Labeled with selenomethionine -

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Basic information

Entry
Database: PDB / ID: 6wb4
TitleMicrobiome-derived Acarbose Kinase Mak1 Labeled with selenomethionine
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 / ADENOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.593 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 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)71,64311
Polymers69,1372
Non-polymers2,5069
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Ribokinase family dimerizes via this beta-clasp domain
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-116 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.831, 123.509, 102.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRchain AAA2 - 29922 - 319
2LEULEUchain BBB-6 - 29914 - 319

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Components

#1: Protein Acarbose Kinase Mak1


Mass: 34568.656 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
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 CaCl2, 6 mM ATP, 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-2 / Wavelength: 0.97932 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.59→29.601 Å / Num. obs: 22619 / % possible obs: 99.4 % / Redundancy: 20.2 % / Biso Wilson estimate: 63.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.03 / Rrim(I) all: 0.134 / Net I/σ(I): 16.9
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
2.59-2.7119.71.4695220626450.8020.3311.5072.295.9
8.98-29.616.80.057100685980.9990.0130.05950.197.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
SHELXphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.593→29.6 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / Phase error: 28.7
RfactorNum. reflection% reflection
Rfree0.2531 1099 4.86 %
Rwork0.1859 --
obs0.1891 22593 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.98 Å2 / Biso mean: 76.972 Å2 / Biso min: 32.3 Å2
Refinement stepCycle: final / Resolution: 2.593→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 155 19 4721
Biso mean--127.2 63.85 -
Num. residues----604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114823
X-RAY DIFFRACTIONf_angle_d1.0226581
X-RAY DIFFRACTIONf_chiral_restr0.042759
X-RAY DIFFRACTIONf_plane_restr0.005837
X-RAY DIFFRACTIONf_dihedral_angle_d13.3761719
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2456X-RAY DIFFRACTION10.165TORSIONAL
12B2456X-RAY DIFFRACTION10.165TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5934-2.71130.30421350.2556255396
2.7113-2.85420.3251330.24422654100
2.8542-3.03280.3131340.24352674100
3.0328-3.26670.30981330.21892676100
3.2667-3.5950.26681460.19442675100
3.595-4.1140.23371410.17642709100
4.114-5.17870.20551450.15482714100
5.1787-29.60.2541320.17492839100
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)
10.1594-0.08890.59070.10950.40860.25540.1894-0.18650.09610.28520.036-0.0773-0.0628-0.11750.01170.62510.0487-0.00010.51130.07490.588936.835345.210533.9131
20.37190.5720.05850.83630.07280.01960.7228-0.30030.91090.80460.09580.0725-0.19380.21020.1430.64550.11380.01190.53990.03210.53939.953739.141.3493
30.08120.03920.02040.07280.10970.13940.1062-0.2469-0.64280.4304-0.08010.40760.5613-0.44340.00060.74950.15590.00950.45690.03020.553824.491145.781425.5543
40.6005-0.32620.34740.50010.30280.29010.12310.0882-0.2285-0.1006-0.0155-0.03010.3993-0.2742-0.00010.6440.10.00130.4440.08520.595632.863241.313623.8138
50.16840.29160.28370.53830.63550.5438-0.07890.17810.12-0.21170.0515-0.10650.31730.140200.42530.1194-0.00370.48040.04220.509933.189258.23115.1234
60.22350.18990.11890.94310.57980.4589-0.3354-0.30560.0712-0.03710.7619-0.1062-0.39630.71970.20930.54430.1942-0.07830.7101-0.05170.496830.89467.513628.1484
70.33280.2679-0.29290.2762-0.16820.4169-0.4611-0.17070.05780.14390.6065-0.31780.6166-0.19810.0210.61110.2392-0.12220.6557-0.06330.595822.900462.223729.4288
80.60690.1035-0.15250.0368-0.15411.4362-0.24550.2184-0.18441.35570.1755-0.26840.8544-0.8051-0.18520.76350.2794-0.15130.7109-0.04810.583821.330457.434139.444
9-0.0627-0.0882-0.01260.36460.29590.6541-0.06940.0264-0.015-0.33620.098-0.11390.1624-0.187-0.00010.4836-0.02760.00090.357-0.00410.46746.58825.246337.6879
100.3762-0.4705-0.31870.25980.27430.7771-0.10.0503-0.12660.05120.03410.1074-0.17-0.07200.43520.006-0.0740.38610.01420.362943.857623.2436.6999
110.8199-0.15160.49870.3536-0.18610.9888-0.087-0.10010.10470.40460.095-0.05210.0250.07310.00110.42670.05780.03230.4116-0.01980.401646.223419.858349.1485
120.86260.0365-0.39770.10280.21670.4441-0.1575-0.49180.01640.10890.260.14260.210.39650.00040.48290.061-0.1120.6591-0.09570.420661.886320.193454.5454
130.30960.47820.1453.09571.18750.470.291-0.38210.7833-0.82760.523-0.1764-0.75160.8260.6591-0.06450.039-0.0130.6458-0.13050.483370.411120.747441.0059
140.69350.1075-0.73160.25950.11690.66590.0392-0.07860.2998-0.12970.1120.00430.18760.062-0.00010.39570.0704-0.07040.4752-0.02390.511764.049414.026736.0877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 29 )A2 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 42 )A30 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 67 )A43 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 130 )A68 - 130
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 201 )A131 - 201
6X-RAY DIFFRACTION6chain 'A' and (resid 202 through 244 )A202 - 244
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 279 )A245 - 279
8X-RAY DIFFRACTION8chain 'A' and (resid 280 through 299 )A280 - 299
9X-RAY DIFFRACTION9chain 'B' and (resid -6 through 29 )B-6 - 29
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 100 )B30 - 100
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 152 )B101 - 152
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 220 )B153 - 220
13X-RAY DIFFRACTION13chain 'B' and (resid 221 through 244 )B221 - 244
14X-RAY DIFFRACTION14chain 'B' and (resid 245 through 299 )B245 - 299

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