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- PDB-7ye3: Crystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-he... -

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Basic information

Entry
Database: PDB / ID: 7ye3
TitleCrystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MES
Components4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / pectin catabolic process / zinc ion binding
Similarity search - Function
5-keto 4-deoxyuronate isomerase / 5-keto-4-deoxyuronate isomerase, N-terminal / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Similarity search - Component
Biological speciesLacticaseibacillus rhamnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.553 Å
AuthorsYamamoto, Y. / Oiki, S. / Takase, R. / Mikami, B. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J Appl Glycosci (1999) / Year: 2023
Title: Crystal Structures of Lacticaseibacillus 4-Deoxy-L- threo- 5-hexosulose-uronate Ketol-isomerase KduI in Complex with Substrate Analogs.
Authors: Iwase, H. / Yamamoto, Y. / Yamada, A. / Kawai, K. / Oiki, S. / Watanabe, D. / Mikami, B. / Takase, R. / Hashimoto, W.
History
DepositionJul 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,16316
Polymers199,9906
Non-polymers1,17310
Water1629
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.035, 189.102, 114.852
Angle α, β, γ (deg.)90.000, 107.120, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2:195 or resseq 200 or resseq 202:267))
21(chain B and (resseq 2:195 or resseq 200 or resseq 202:267))
31(chain C and (resseq 2:195 or resseq 200 or resseq 202:267))
41chain D
51(chain E and (resseq 2:195 or resseq 200 or resseq 202:267))
61(chain F and (resseq 2:195 or resseq 200 or resseq 202:267))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERMETMET(chain A and (resseq 2:195 or resseq 200 or resseq 202:267))AA2 - 1952 - 195
12HISHISHISHIS(chain A and (resseq 2:195 or resseq 200 or resseq 202:267))AA200200
13ARGARGGLNGLN(chain A and (resseq 2:195 or resseq 200 or resseq 202:267))AA202 - 267202 - 267
21SERSERMETMET(chain B and (resseq 2:195 or resseq 200 or resseq 202:267))BB2 - 1952 - 195
22HISHISHISHIS(chain B and (resseq 2:195 or resseq 200 or resseq 202:267))BB200200
23ARGARGGLNGLN(chain B and (resseq 2:195 or resseq 200 or resseq 202:267))BB202 - 267202 - 267
31SERSERMETMET(chain C and (resseq 2:195 or resseq 200 or resseq 202:267))CC2 - 1952 - 195
32HISHISHISHIS(chain C and (resseq 2:195 or resseq 200 or resseq 202:267))CC200200
33ARGARGGLNGLN(chain C and (resseq 2:195 or resseq 200 or resseq 202:267))CC202 - 267202 - 267
41SERSERGLNGLNchain DDD2 - 2672 - 267
51SERSERMETMET(chain E and (resseq 2:195 or resseq 200 or resseq 202:267))EE2 - 1952 - 195
52HISHISHISHIS(chain E and (resseq 2:195 or resseq 200 or resseq 202:267))EE200200
53ARGARGGLNGLN(chain E and (resseq 2:195 or resseq 200 or resseq 202:267))EE202 - 267202 - 267
61SERSERMETMET(chain F and (resseq 2:195 or resseq 200 or resseq 202:267))FF2 - 1952 - 195
62HISHISHISHIS(chain F and (resseq 2:195 or resseq 200 or resseq 202:267))FF200200
63ARGARGGLNGLN(chain F and (resseq 2:195 or resseq 200 or resseq 202:267))FF202 - 267202 - 267

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Components

#1: Protein
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase / 5-keto-4-deoxyuronate isomerase / DKI isomerase


Mass: 33331.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lacticaseibacillus rhamnosus (bacteria)
Gene: kduI, HMPREF0539_0625 / Production host: Escherichia coli (E. coli)
References: UniProt: C2JUP1, 5-dehydro-4-deoxy-D-glucuronate isomerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES (pH 6.5), 1 mM 4-deoxy-L-threo-5-hexosulose-uronate, 1 mM rhamnose, 12% PEG 4000, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 60742 / % possible obs: 98.3 % / Redundancy: 3.38 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.34
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 3.51 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 19187 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E4S

7e4s


Resolution: 2.553→37.567 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.35 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2558 3029 4.99 %
Rwork0.1933 57649 -
obs0.1965 60678 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.15 Å2 / Biso mean: 86.2976 Å2 / Biso min: 39.37 Å2
Refinement stepCycle: final / Resolution: 2.553→37.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13229 0 54 9 13292
Biso mean--120.4 69.17 -
Num. residues----1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813627
X-RAY DIFFRACTIONf_angle_d1.1118453
X-RAY DIFFRACTIONf_chiral_restr0.0671943
X-RAY DIFFRACTIONf_plane_restr0.0082393
X-RAY DIFFRACTIONf_dihedral_angle_d17.7588071
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7664X-RAY DIFFRACTION18.63TORSIONAL
12B7664X-RAY DIFFRACTION18.63TORSIONAL
13C7664X-RAY DIFFRACTION18.63TORSIONAL
14D7664X-RAY DIFFRACTION18.63TORSIONAL
15E7664X-RAY DIFFRACTION18.63TORSIONAL
16F7664X-RAY DIFFRACTION18.63TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.553-2.59290.47021340.3666255497
2.5929-2.63540.41921380.3521263899
2.6354-2.68080.4461340.3312255399
2.6808-2.72950.38371390.31262599
2.7295-2.7820.38041370.2851259999
2.782-2.83880.32751380.2738263299
2.8388-2.90050.38651370.274263199
2.9005-2.96790.34671350.2721259299
2.9679-3.04210.37271390.2552262899
3.0421-3.12430.31851370.2499262199
3.1243-3.21620.34631370.2506259299
3.2162-3.320.32111390.2427265699
3.32-3.43860.30431360.244260899
3.4386-3.57610.29831390.2325264199
3.5761-3.73880.30211390.2153263899
3.7388-3.93570.27911380.2004261499
3.9357-4.18190.25431390.1789264799
4.1819-4.50440.20621370.1429260999
4.5044-4.95670.16111380.1316260498
4.9567-5.67190.18851380.1461263899
5.6719-7.13790.22341400.1623265499
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)
10.4755-0.09430.11030.16210.07130.3497-0.30160.1826-0.14160.01340.2240.19920.0353-0.1537-00.5857-0.17480.03790.5098-0.09320.583916.7425-94.97422.1381
2-0.00680.00140.0199-0.00480.03080.0298-0.325-0.2688-0.25860.33430.420.23650.2448-0.1076-0.00010.9021-0.02940.19880.82190.08810.90485.9721-94.626339.401
30.1116-0.0223-0.09150.0876-0.03490.0322-0.2608-0.06420.17840.24170.30930.36490.1912-0.1344-0.00010.5502-0.0528-0.01740.58540.04950.536710.6485-81.856635.0055
40.131-0.1099-0.13480.08740.10560.0927-0.1729-0.1135-0.03750.04980.25490.13160.1392-0.187100.6162-0.0006-0.03210.67250.0330.594214.8314-83.170735.8598
50.82410.1458-0.02050.0701-0.06540.4954-0.1978-0.2959-0.1455-0.1267-0.0531-0.24750.09620.115-0.00340.59750.0960.10570.49690.11950.464944.5632-96.155140.3552
60.0232-0.0106-0.04810.2196-0.03160.0947-0.1672-0.1841-0.0237-0.3162-0.0062-0.20770.19730.0957-0.00010.76020.05260.09250.59810.00140.59151.1145-88.475627.5375
70.03380.00660.0048-0.0045-0.00430.0301-0.1009-0.086-0.1154-0.08850.0498-0.09410.28470.2318-0.00010.96420.00820.09670.6194-0.06890.723543.038-95.138121.8295
80.0682-0.06760.12010.0994-0.00150.13440.0130.089-0.15-0.003-0.06260.082-0.0904-0.3698-0.00010.6973-0.0324-0.00950.5645-0.09770.602653.2011-64.48889.1123
90.1033-0.01760.10.0122-0.00790.0819-0.08360.13210.3448-0.0721-0.0159-0.25440.07480.049400.7864-0.04370.12270.4853-0.02920.616468.2125-62.4594-4.5388
100.1279-0.0888-0.0010.06440.09720.0361-0.0607-0.08550.1733-0.1288-0.0989-0.29890.34990.2157-00.8767-0.04650.17030.5482-0.13650.778669.247-63.6315-3.2335
110.045-0.0565-0.02710.0489-0.02860.00360.16730.0698-0.3622-0.02040.02010.0034-0.11220.05970.00270.73360.03560.10440.72910.02551.034976.1498-79.277513.5244
120.1448-0.06210.0510.07340.070.0893-0.1512-0.28730.0448-0.0478-0.1804-0.39070.12020.055-0.00020.73010.0090.17820.5987-0.0950.819170.1539-71.218814.5533
130.04450.03070.07060.0318-0.05590.1336-0.3589-0.2894-0.1731-0.2210.0621-0.18480.23880.1262-0.00030.8-0.01070.10220.5659-0.1280.565757.4246-76.275915.9991
140.04660.0161-0.04320.0485-0.02320.014-0.2014-0.03760.15360.16610.1292-0.06460.0225-0.11050.00010.73890.07130.03910.7835-0.1550.932767.918-67.259721.981
150.0581-0.09210.08710.2318-0.19570.6384-0.2027-0.30110.3860.05490.2265-0.38570.12480.1125-0.03470.45670.0681-0.15660.5642-0.28870.986765.2962-41.140225.8398
160.01210.0354-0.04560.0884-0.14130.1040.03850.2520.1329-0.1838-0.0342-0.4624-0.0518-0.1716-0.00020.57790.0134-0.00830.6322-0.16811.007357.494-29.412211.771
170.0707-0.13360.00480.13540.0160.0223-0.2529-0.14310.27910.1980.2104-0.3240.0736-0.06460.00020.568-0.0017-0.07610.5804-0.18350.757149.598-37.512419.3216
180.43950.6157-0.29630.8377-0.70310.43730.0057-0.0219-0.11640.25970.21240.1654-0.1706-0.033200.64850.15030.0130.59590.03670.46035.2204-46.859444.6472
190.0239-0.03130.0280.0328-0.01770.01110.02490.2008-0.22420.04680.18430.4779-0.2732-0.3938-0.00030.79090.10660.13120.76480.19440.7044-0.3099-60.435835.7477
200.02560.0786-0.00540.07970.00640.0036-0.14660.0324-0.23550.03220.12990.30610.1357-0.2162-0.00010.5970.1122-0.00540.69280.08310.61047.1017-60.170536.633
210.2761-0.02610.1680.88110.19720.3412-0.85690.8172-0.46860.05440.5668-0.28120.5523-0.8476-0.36140.516-0.2458-0.09751.2174-0.14210.360817.2147-43.185214.5371
220.11690.07280.30870.59520.3410.761-0.16670.76370.3835-0.0094-0.13530.05790.18030.138-0.55180.5301-0.0323-0.17611.5690.48740.61844.6109-30.478713.3948
230.01240.14770.08130.90930.23950.92370.15481.20080.84020.23741.08210.3721-0.655-0.42161.95590.15790.2109-0.31241.10050.62090.400913.7357-24.593417.0839
240.00250.0028-0.0134-0.0211-0.01330.02520.00840.17010.27650.03430.2435-0.4289-0.1798-0.22910.00050.49240.1121-0.1190.84520.19110.758828.5441-24.587319.0895
250.03860.02950.01970.01160.0160.0081-0.32890.0176-0.05420.69380.0340.1244-0.0911-0.04470.00010.8210.089-0.0860.93790.07980.653222.7114-33.140725.0028
260.11970.1315-0.08140.025-0.09930.0713-0.57570.598-0.07540.08490.4359-0.291-0.1015-0.442700.6264-0.0268-0.04970.7609-0.07350.426529.0864-34.834618.0253
27-0.00220.00010.00020.0119-0.0232-0.00390.0157-0.14530.1074-0.2590.00910.11640.06670.2694-0.00011.02380.0058-0.01361.4904-0.17041.270525.4594-30.249633.8925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 141 )A2 - 141
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 179 )A142 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 229 )A180 - 229
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 279 )A230 - 279
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 179 )B2 - 179
6X-RAY DIFFRACTION6chain 'B' and (resid 180 through 256 )B180 - 256
7X-RAY DIFFRACTION7chain 'B' and (resid 257 through 280 )B257 - 280
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 54 )C2 - 54
9X-RAY DIFFRACTION9chain 'C' and (resid 55 through 108 )C55 - 108
10X-RAY DIFFRACTION10chain 'C' and (resid 109 through 141 )C109 - 141
11X-RAY DIFFRACTION11chain 'C' and (resid 142 through 162 )C142 - 162
12X-RAY DIFFRACTION12chain 'C' and (resid 163 through 210 )C163 - 210
13X-RAY DIFFRACTION13chain 'C' and (resid 211 through 256 )C211 - 256
14X-RAY DIFFRACTION14chain 'C' and (resid 257 through 280 )C257 - 280
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 141 )D2 - 141
16X-RAY DIFFRACTION16chain 'D' and (resid 142 through 202 )D142 - 202
17X-RAY DIFFRACTION17chain 'D' and (resid 203 through 267 )D203 - 267
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 179 )E2 - 179
19X-RAY DIFFRACTION19chain 'E' and (resid 180 through 202 )E180 - 202
20X-RAY DIFFRACTION20chain 'E' and (resid 203 through 280 )E203 - 280
21X-RAY DIFFRACTION21chain 'F' and (resid 2 through 65 )F2 - 65
22X-RAY DIFFRACTION22chain 'F' and (resid 66 through 108 )F66 - 108
23X-RAY DIFFRACTION23chain 'F' and (resid 109 through 179 )F109 - 179
24X-RAY DIFFRACTION24chain 'F' and (resid 180 through 196 )F180 - 196
25X-RAY DIFFRACTION25chain 'F' and (resid 197 through 210 )F197 - 210
26X-RAY DIFFRACTION26chain 'F' and (resid 211 through 264 )F211 - 264
27X-RAY DIFFRACTION27chain 'F' and (resid 265 through 279 )F265 - 279

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