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

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Entry
Database: PDB / ID: 7yrs
TitleCrystal structure of Lactobacillus rhamnosus 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase KduI complexed with MOPS
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: 2.802 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
DepositionAug 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: 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 1.2Jan 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

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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)201,21916
Polymers199,9906
Non-polymers1,23010
Water00
1
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6063
Polymers33,3321
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-32 kcal/mol
Surface area12510 Å2
MethodPISA
2
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6063
Polymers33,3321
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-33 kcal/mol
Surface area12060 Å2
MethodPISA
3
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3972
Polymers33,3321
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-39 kcal/mol
Surface area12460 Å2
MethodPISA
4
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3972
Polymers33,3321
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area11890 Å2
MethodPISA
5
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6063
Polymers33,3321
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-30 kcal/mol
Surface area12510 Å2
MethodPISA
6
F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6063
Polymers33,3321
Non-polymers2752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-32 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.404, 187.400, 108.934
Angle α, β, γ (deg.)90.000, 112.490, 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 200:266))
21(chain B and (resseq 2:195 or resseq 200:266))
31(chain C and (resseq 2:195 or resseq 200:266))
41(chain E and (resseq 2:195 or resseq 200:266))
51(chain F and (resseq 2:195 or resseq 200:266))
61chain D

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 200:266))AA2 - 1952 - 195
12HISHISASNASN(chain A and (resseq 2:195 or resseq 200:266))AA200 - 266200 - 266
21SERSERMETMET(chain B and (resseq 2:195 or resseq 200:266))BB2 - 1952 - 195
22HISHISASNASN(chain B and (resseq 2:195 or resseq 200:266))BB200 - 266200 - 266
31SERSERMETMET(chain C and (resseq 2:195 or resseq 200:266))CC2 - 1952 - 195
32HISHISASNASN(chain C and (resseq 2:195 or resseq 200:266))CC200 - 266200 - 266
41SERSERMETMET(chain E and (resseq 2:195 or resseq 200:266))EE2 - 1952 - 195
42HISHISASNASN(chain E and (resseq 2:195 or resseq 200:266))EE200 - 266200 - 266
51SERSERMETMET(chain F and (resseq 2:195 or resseq 200:266))FF2 - 1952 - 195
52HISHISASNASN(chain F and (resseq 2:195 or resseq 200:266))FF200 - 266200 - 266
61SERSERASNASNchain DDD2 - 2662 - 266

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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-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MOPS (pH 6.5), 1 mM 4-deoxy-L-threo-5-hexosulose-uronate, 1 mM rhamnose, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 40666 / % possible obs: 96.2 % / Redundancy: 2.02 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 6.36
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 12569 / % possible all: 96.1

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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: 2.802→49.549 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2648 2034 5 %
Rwork0.1888 38610 -
obs0.1926 40644 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.17 Å2 / Biso mean: 82.5576 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.802→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13246 0 58 0 13304
Biso mean--105.6 --
Num. residues----1647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313645
X-RAY DIFFRACTIONf_angle_d1.74118479
X-RAY DIFFRACTIONf_chiral_restr0.1051946
X-RAY DIFFRACTIONf_plane_restr0.0132395
X-RAY DIFFRACTIONf_dihedral_angle_d18.4488081
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7520X-RAY DIFFRACTION17.853TORSIONAL
12B7520X-RAY DIFFRACTION17.853TORSIONAL
13C7520X-RAY DIFFRACTION17.853TORSIONAL
14E7520X-RAY DIFFRACTION17.853TORSIONAL
15F7520X-RAY DIFFRACTION17.853TORSIONAL
16D7520X-RAY DIFFRACTION17.853TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8024-2.86760.43181310.3178247796
2.8676-2.93930.38671350.28232566100
2.9393-3.01880.38351380.27232613100
3.0188-3.10760.38281350.26262576100
3.1076-3.20790.3171370.24272597100
3.2079-3.32250.33531350.232557100
3.3225-3.45550.33961370.22342597100
3.4555-3.61270.33631370.20832613100
3.6127-3.80310.30621340.1977255099
3.8031-4.04130.22891360.1798257199
4.0413-4.35310.25231340.1592255098
4.3531-4.79090.22861340.138254898
4.7909-5.48340.20461360.1504257399
5.4834-6.90550.21531360.1793259199
6.9055-49.50.21261390.17262631100
Refinement TLS params.Method: refined / Origin x: 9.9388 Å / Origin y: 0.0503 Å / Origin z: 25.3282 Å
111213212223313233
T0.4026 Å20.0268 Å20.032 Å2-0.4389 Å20.0819 Å2--0.4194 Å2
L0.6078 °20.2365 °20.0761 °2-1.1176 °20.0666 °2--0.3161 °2
S-0.0738 Å °0.0203 Å °0.0917 Å °-0.0419 Å °-0.0073 Å °0.2351 Å °-0.0027 Å °0.0008 Å °0.08 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 280
2X-RAY DIFFRACTION1allB2 - 279
3X-RAY DIFFRACTION1allC2 - 280
4X-RAY DIFFRACTION1allD2 - 266
5X-RAY DIFFRACTION1allE2 - 279
6X-RAY DIFFRACTION1allF2 - 280
7X-RAY DIFFRACTION1allG301 - 306
8X-RAY DIFFRACTION1allH1 - 4

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