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- PDB-8gst: Crystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase fro... -

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Basic information

Entry
Database: PDB / ID: 8gst
TitleCrystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (pyruvate bound-form)
ComponentsL-2,4-diketo-3-deoxyrhamnonate hydrolase
KeywordsHYDROLASE / FAH protein superfamily / hydroxyacylpyruvate
Function / homologyPYRUVIC ACID
Function and homology information
Biological speciesSphingomonas sp. SKA58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsFukuhara, S. / Watanabe, Y. / Watanabe, S. / Nishiwaki, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Crystal Structure of l-2,4-Diketo-3-deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated l-Rhamnose Pathway from Bacteria.
Authors: Fukuhara, S. / Watanabe, S. / Watanabe, Y. / Nishiwaki, H.
History
DepositionSep 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-2,4-diketo-3-deoxyrhamnonate hydrolase
B: L-2,4-diketo-3-deoxyrhamnonate hydrolase
C: L-2,4-diketo-3-deoxyrhamnonate hydrolase
D: L-2,4-diketo-3-deoxyrhamnonate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,56410
Polymers129,3544
Non-polymers2106
Water21,7981210
1
A: L-2,4-diketo-3-deoxyrhamnonate hydrolase
B: L-2,4-diketo-3-deoxyrhamnonate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7264
Polymers64,6772
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-26 kcal/mol
Surface area22050 Å2
MethodPISA
2
C: L-2,4-diketo-3-deoxyrhamnonate hydrolase
D: L-2,4-diketo-3-deoxyrhamnonate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8386
Polymers64,6772
Non-polymers1614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-26 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.254, 66.228, 75.256
Angle α, β, γ (deg.)90.270, 91.430, 105.200
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-2,4-diketo-3-deoxyrhamnonate hydrolase


Mass: 32338.535 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas sp. SKA58 (bacteria) / Strain: SKA58 / Production host: Escherichia coli DH5[alpha] (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1210 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50% PEG 3350, 200 mM MgCl2, 100 mM Tris-HCl pH 8.5

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→48.99 Å / Num. obs: 125104 / % possible obs: 96.7 % / Redundancy: 5 % / Biso Wilson estimate: 20.72 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.08 / Rrim(I) all: 0.171 / Net I/σ(I): 12.6 / Num. measured all: 623308 / Scaling rejects: 43193
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
1.71-1.745.41.223338561590.7370.5731.352.595.8
9.37-48.995.30.05340947780.9960.0250.05932.398.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GSR

8gsr


Resolution: 1.71→48.988 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 6299 5.04 %
Rwork0.1796 118561 -
obs0.1814 124860 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.45 Å2 / Biso mean: 26.2387 Å2 / Biso min: 5.22 Å2
Refinement stepCycle: final / Resolution: 1.71→48.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8726 0 11 1210 9947
Biso mean--21.77 32.58 -
Num. residues----1151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068917
X-RAY DIFFRACTIONf_angle_d0.8612113
X-RAY DIFFRACTIONf_chiral_restr0.0591344
X-RAY DIFFRACTIONf_plane_restr0.0061607
X-RAY DIFFRACTIONf_dihedral_angle_d7.7225320
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.71-1.72940.29162320.2597393596
1.7294-1.74980.27952530.2562389096
1.7498-1.77110.32042230.245387096
1.7711-1.79350.26972580.2335392096
1.7935-1.81710.26922140.2228388996
1.8171-1.8420.24681950.2188399496
1.842-1.86840.27342080.2051385396
1.8684-1.89620.25752310.2061400096
1.8962-1.92590.24942180.2024390696
1.9259-1.95750.25552200.1966392996
1.9575-1.99120.24312220.2018391096
1.9912-2.02740.25022130.2002391596
2.0274-2.06640.22241960.1833392596
2.0664-2.10860.24342240.1928385195
2.1086-2.15440.26742190.1938395796
2.1544-2.20460.25721800.1944397896
2.2046-2.25970.22761930.1969385095
2.2597-2.32080.21712260.19386495
2.3208-2.38910.2442170.192398096
2.3891-2.46620.23562060.201391296
2.4662-2.55430.2582020.1972392796
2.5543-2.65660.24641880.197397096
2.6566-2.77750.21961650.1883401996
2.7775-2.92390.21241910.1846398497
2.9239-3.10710.21662210.187399398
3.1071-3.34690.2051640.1801411098
3.3469-3.68360.19611990.1642403799
3.6836-4.21640.17092010.1338406199
4.2164-5.31120.1471760.1308409699
5.3112-48.9880.18832440.1636403699

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