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- PDB-7x7w: The X-ray Crystallographic Structure of D-Psicose 3-epimerase fro... -

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Basic information

Entry
Database: PDB / ID: 7x7w
TitleThe X-ray Crystallographic Structure of D-Psicose 3-epimerase from Clostridia bacterium
ComponentsD-PSICOSE 3-EPIMERASE
KeywordsISOMERASE / D-Psicose 3-epimerase
Function / homology:
Function and homology information
Biological speciesClostridia bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsLi, Z.F. / Ban, X.F. / Xie, X.F. / Tian, Y.X. / Li, C.M. / Gu, Z.B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722040 China
National Natural Science Foundation of China (NSFC)31771935 China
National Natural Science Foundation of China (NSFC)31901628 China
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2022
Title: Crystal structure of a novel homodimeric D-allulose 3-epimerase from a Clostridia bacterium
Authors: Xie, X. / Tian, Y. / Ban, X. / Li, C. / Yang, H. / Li, Z.
History
DepositionMar 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-PSICOSE 3-EPIMERASE
B: D-PSICOSE 3-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8074
Polymers64,6972
Non-polymers1102
Water2,900161
1
A: D-PSICOSE 3-EPIMERASE
hetero molecules

B: D-PSICOSE 3-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8074
Polymers64,6972
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3070 Å2
ΔGint-14 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.018, 70.657, 153.784
Angle α, β, γ (deg.)90.000, 99.320, 90.000
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-498-

HOH

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Components

#1: Protein D-PSICOSE 3-EPIMERASE


Mass: 32348.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridia bacterium (bacteria) / Production host: Bacillus subtilis (bacteria)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Succine acid pH 7.0, 0.1 M HEPES pH7.0, 1% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.09→37.95 Å / Num. obs: 37135 / % possible obs: 99.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.68 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 30.4
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.124 / Num. unique obs: 2994

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VNK

3vnk


Resolution: 2.097→37.939 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 34.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1993 5.42 %
Rwork0.2 34760 -
obs0.2029 36753 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96 Å2 / Biso mean: 50.2439 Å2 / Biso min: 27.64 Å2
Refinement stepCycle: final / Resolution: 2.097→37.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 2 161 4705
Biso mean--49.86 45.43 -
Num. residues----576
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.097-2.14930.36221380.2681245497
2.1493-2.20740.31781400.2542247099
2.2074-2.27240.36891420.2504247999
2.2724-2.34570.31291410.2295247199
2.3457-2.42960.27841430.2356247898
2.4296-2.52680.31281400.2273240895
2.5268-2.64180.2931420.239248599
2.6418-2.7810.30281440.23932487100
2.781-2.95520.29991430.2382250999
2.9552-3.18330.29841430.2349247898
3.1833-3.50340.28121420.2086247198
3.5034-4.00990.24011450.1889252499
4.0099-5.05010.18161440.1558249498
5.0501-37.9390.19791460.1572255298

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