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- PDB-3p12: Crystal Structure of D-ribose Pyranase Sa240 -

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Basic information

Entry
Database: PDB / ID: 3p12
TitleCrystal Structure of D-ribose Pyranase Sa240
ComponentsD-ribose pyranase
KeywordsISOMERASE / RbsD / D-ribose Pyranase / Sa240 / Carbohydrate metabolism
Function / homology
Function and homology information


D-ribose pyranase / D-ribose pyranase activity / intramolecular transferase activity / intramolecular lyase activity / D-ribose catabolic process / monosaccharide binding / cytosol
Similarity search - Function
D-ribose pyranase / RbsD-like fold / RbsD-like domain / D-ribose pyranase RbsD/L-fucose mutarotase FucU / RbsD-like superfamily / RbsD / FucU transport protein family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsWu, M. / Wang, L. / Zang, J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Crystal structure of Sa240: A ribose pyranase homolog with partial active site from Staphylococcus aureus
Authors: Wang, L. / Wu, M. / Zang, J.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: D-ribose pyranase
B: D-ribose pyranase
C: D-ribose pyranase
D: D-ribose pyranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1448
Polymers65,7754
Non-polymers3684
Water3,927218
1
A: D-ribose pyranase
D: D-ribose pyranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0724
Polymers32,8882
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-8 kcal/mol
Surface area11710 Å2
MethodPISA
2
B: D-ribose pyranase
C: D-ribose pyranase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0724
Polymers32,8882
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.126, 122.126, 175.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
D-ribose pyranase


Mass: 16443.842 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: rbsD, SAOUHSC_00240 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q2G1A5, Isomerases; Intramolecular lyases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH 4.6, 2.0M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794, 0.9795, 1.0000
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
311
ReflectionResolution: 2.35→50 Å / Num. all: 32992 / Num. obs: 32949 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.088 / Net I/σ(I): 30.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1586 / Rsym value: 0.334 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→42.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / Cross valid method: THROUGHOUT / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25199 1670 5.1 %RANDOM
Rwork0.2173 ---
all0.21896 31237 --
obs0.21896 31215 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.47 Å20 Å2
2---0.94 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.35→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 24 218 4348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9725785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5085531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.33926.01198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.11415792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.3251516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213133
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1261.52618
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.33124310
X-RAY DIFFRACTIONr_scbond_it2.70531636
X-RAY DIFFRACTIONr_scangle_it4.5444.51465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 115 -
Rwork0.284 2247 -
obs--99.92 %

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