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- PDB-3exs: Crystal structure of KGPDC from Streptococcus mutans in complex w... -

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Basic information

Entry
Database: PDB / ID: 3exs
TitleCrystal structure of KGPDC from Streptococcus mutans in complex with D-R5P
ComponentsRmpD (Hexulose-6-phosphate synthase)
KeywordsLYASE / beta barrel
Function / homology
Function and homology information


3-hexulose-6-phosphate synthase / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / metal ion binding
Similarity search - Function
HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RIBULOSE-5-PHOSPHATE / 3-hexulose-6-phosphate synthase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, G.L. / Liu, X. / Wang, K.T. / Li, L.F. / Su, X.D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans
Authors: Li, G.L. / Liu, X. / Nan, J. / Brostromer, E. / Li, L.F. / Su, X.D.
History
DepositionOct 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RmpD (Hexulose-6-phosphate synthase)
B: RmpD (Hexulose-6-phosphate synthase)
C: RmpD (Hexulose-6-phosphate synthase)
D: RmpD (Hexulose-6-phosphate synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8616
Polymers95,4014
Non-polymers4602
Water5,368298
1
A: RmpD (Hexulose-6-phosphate synthase)
C: RmpD (Hexulose-6-phosphate synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9313
Polymers47,7002
Non-polymers2301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-4.3 kcal/mol
Surface area16770 Å2
MethodPISA
2
B: RmpD (Hexulose-6-phosphate synthase)
D: RmpD (Hexulose-6-phosphate synthase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9313
Polymers47,7002
Non-polymers2301
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-7 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.152, 124.249, 130.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RmpD (Hexulose-6-phosphate synthase) / 3-keto-L-gulonate 6-phosphate decarboxylase


Mass: 23850.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: ulaD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93DA8, 3-dehydro-L-gulonate-6-phosphate decarboxylase
#2: Sugar ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M KCl, 0.05M HEPES, pH7.5, 35%(v/v) pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→19.74 Å / Num. obs: 31798 / % possible obs: 93.41 % / Rsym value: 0.077

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EXT

3ext


Resolution: 2.5→19.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.837 / SU B: 9.172 / SU ML: 0.202 / SU R Cruickshank DPI: 0.775 / SU Rfree: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.775 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24386 1548 5 %RANDOM
Rwork0.18357 ---
obs0.18661 29234 90.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.02 Å2 / Biso mean: 22.278 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6339 0 27 298 6664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9558761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3525.379264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.396151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6451530
X-RAY DIFFRACTIONr_chiral_restr0.0940.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.23122
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24483
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8131.54249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2426658
X-RAY DIFFRACTIONr_scbond_it1.90132492
X-RAY DIFFRACTIONr_scangle_it3.0144.52103
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 58 -
Rwork0.261 1289 -
all-1347 -
obs--55.43 %

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