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- PDB-3vnk: Crystal structures of D-Psicose 3-epimerase with D-fructose from ... -

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Basic information

Entry
Database: PDB / ID: 3vnk
TitleCrystal structures of D-Psicose 3-epimerase with D-fructose from Clostridium cellulolyticum H10
ComponentsXylose isomerase domain protein TIM barrel
KeywordsISOMERASE / D-Psicose 3-epimerase / ketohexose / TIM barrrel
Function / homology
Function and homology information


D-psicose 3-epimerase / racemase and epimerase activity, acting on carbohydrates and derivatives / cobalt ion binding / manganese ion binding
Similarity search - Function
: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
D-fructose / : / D-psicose 3-epimerase
Similarity search - Component
Biological speciesClostridium cellulolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Guo, R.T. / Sun, Y.
CitationJournal: Protein Cell / Year: 2012
Title: Crystal structures of D-psicose 3-epimerase from Clostridium cellulolyticum H10 and its complex with ketohexose sugars.
Authors: Chan, H.C. / Zhu, Y. / Hu, Y. / Ko, T.P. / Huang, C.H. / Ren, F. / Chen, C.C. / Ma, Y. / Guo, R.T. / Sun, Y.
History
DepositionJan 16, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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Assembly

Deposited unit
A: Xylose isomerase domain protein TIM barrel
B: Xylose isomerase domain protein TIM barrel
C: Xylose isomerase domain protein TIM barrel
D: Xylose isomerase domain protein TIM barrel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,46516
Polymers132,3054
Non-polymers1,16012
Water17,186954
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-50 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.040, 115.209, 91.375
Angle α, β, γ (deg.)90.00, 105.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Xylose isomerase domain protein TIM barrel


Mass: 33076.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium cellulolyticum (bacteria) / Strain: H10 / Gene: Ccel_0941 / Plasmid: pET-21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8I944
#2: Sugar
ChemComp-FUD / D-fructose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2M tri-sodium citrate dehydrate, 17-20% Polyethylene Glycol 3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→25 Å / Num. obs: 104455 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rsym value: 0.058 / Net I/σ(I): 25.4
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 10428 / Rsym value: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNI

3vni


Resolution: 2.02→25 Å / σ(F): 2
RfactorNum. reflection
Rfree0.227 5062
Rwork0.186 -
all-104660
obs-100158
Refinement stepCycle: LAST / Resolution: 2.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9169 0 56 954 10179

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