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

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Basic information

Entry
Database: PDB / ID: 8gsr
TitleCrystal structure of L-2,4-diketo-3-deoxyrhamnonate hydrolase from Sphingomonas sp. (apo-form)
ComponentsL-2,4-diketo-3-deoxyrhamnonate hydrolase
KeywordsHYDROLASE / FAH protein superfamily / hydroxyacylpyruvate
Biological speciesSphingomonas sp. SKA58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)131,04912
Polymers130,8554
Non-polymers1948
Water22,7351262
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)65,5005
Polymers65,4272
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-36 kcal/mol
Surface area22010 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)65,5497
Polymers65,4272
Non-polymers1225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-30 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.217, 66.412, 75.202
Angle α, β, γ (deg.)90.150, 91.800, 104.940
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 32713.695 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.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1262 / 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: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.73→49.07 Å / Num. obs: 121965 / % possible obs: 97.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 21.91 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.075 / Rrim(I) all: 0.171 / Net I/σ(I): 7 / Num. measured all: 622673 / Scaling rejects: 3248
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
1.73-1.764.91.1132947559930.6150.5591.2491.696
9.48-49.075.50.06941387500.9940.0320.07617.798.4

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 1.73→49.07 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2048 6004 4.94 %
Rwork0.1675 115595 -
obs0.1693 121599 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.81 Å2 / Biso mean: 26.7601 Å2 / Biso min: 5.72 Å2
Refinement stepCycle: final / Resolution: 1.73→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8721 0 8 1262 9991
Biso mean--23.75 33.75 -
Num. residues----1150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078907
X-RAY DIFFRACTIONf_angle_d0.85412101
X-RAY DIFFRACTIONf_chiral_restr0.0591344
X-RAY DIFFRACTIONf_plane_restr0.0061604
X-RAY DIFFRACTIONf_dihedral_angle_d7.6255317
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.73-1.74970.28662060.258379996
1.7497-1.77020.28551800.2366382896
1.7702-1.79180.23441980.2158387696
1.7918-1.81450.26141910.2099375797
1.8145-1.83840.25962260.2054388497
1.8384-1.86360.25311970.2025375996
1.8636-1.89020.22891910.2048392897
1.8902-1.91840.29631620.2349365193
1.9184-1.94840.24411810.225375593
1.9484-1.98030.2722000.1997383096
1.9803-2.01450.24842090.1964383897
2.0145-2.05110.22212190.1872380697
2.0511-2.09060.23472210.1789386897
2.0906-2.13320.21282050.18382597
2.1332-2.17960.22441710.1688388897
2.1796-2.23030.19311670.1706390497
2.2303-2.28610.23321830.1845385996
2.2861-2.34790.20011870.1689387298
2.3479-2.4170.21432350.1745383398
2.417-2.4950.2342170.1785387898
2.495-2.58420.22332370.179388898
2.5842-2.68760.21122070.1705386798
2.6876-2.810.22881730.1751391698
2.81-2.95810.21771840.1714395198
2.9581-3.14340.19052280.1699386998
3.1434-3.3860.20552070.1673387898
3.386-3.72670.20152020.1559392098
3.7267-4.26570.1561760.1279386097
4.2657-5.37320.13671930.1234393698
5.3732-49.070.1822510.1516387299

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