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- PDB-7vpf: Crystal structure of a novel putative sugar isomerase from the ps... -

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Basic information

Entry
Database: PDB / ID: 7vpf
TitleCrystal structure of a novel putative sugar isomerase from the psychrophilic bacterium Paenibacillus sp. R4
ComponentsXylose isomerase
KeywordsISOMERASE / sugar isomerase / xylose isomeras / glucose isomerase / Paenibacillus / psychrophilic bacteria / cold adaptation
Function / homology: / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / metal ion binding / Xylose isomerase
Function and homology information
Biological speciesPaenibacillus sp. FSL H7-0331 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.983 Å
AuthorsPark, H.H. / Lee, J.H. / Kwon, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1G1A1100765 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Crystal structure of a novel putative sugar isomerase from the psychrophilic bacterium Paenibacillus sp. R4.
Authors: Kwon, S. / Ha, H.J. / Kang, Y.J. / Sung, J.H. / Hwang, J. / Lee, M.J. / Lee, J.H. / Park, H.H.
History
DepositionOct 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4416
Polymers65,2302
Non-polymers2114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-86 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.932, 141.932, 76.701
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 273)
21(chain B and resid 1 through 273)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 1 - 273 / Label seq-ID: 21 - 293

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 1 through 273)AA
2(chain B and resid 1 through 273)BB

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Components

#1: Protein Xylose isomerase


Mass: 32615.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. FSL H7-0331 (bacteria)
Gene: BK127_09920 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1R1C9D1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium Fluoride, 0.1 M Bis-Tris propane (pH 7.5), 20% PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 11523 / % possible obs: 98.3 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.036 / Rrim(I) all: 0.118 / Χ2: 0.921 / Net I/σ(I): 34.4 / Num. measured all: 117028
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.98-3.0510.10.3757590.9620.1220.3940.85599.7
3.05-3.139.90.3417690.9690.1120.360.83499
3.13-3.219.90.3017990.970.0990.3170.84499.6
3.21-3.310.30.2347790.9840.0750.2460.837100
3.3-3.4110.70.1987770.9820.0630.2080.81799.6
3.41-3.5310.50.1647790.9920.0520.1730.84799.4
3.53-3.6710.30.1437730.9920.0460.150.90299.7
3.67-3.84100.147840.9910.0450.1470.96499.5
3.84-4.049.40.1117880.9950.0370.1170.83599.5
4.04-4.39.40.1017590.9950.0330.1060.92999.2
4.3-4.639.50.1017790.9940.0340.1071.05599
4.63-5.099.90.0887850.9960.0280.0930.81598.9
5.09-5.83110.0917640.9950.0280.0951.15399.7
5.83-7.3411.30.0927900.9950.0280.0961.12599.9
7.34-1010.10.0976390.9890.0330.1020.97281.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QC0

3qc0


Resolution: 2.983→26.823 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 542 4.73 %
Rwork0.214 10914 -
obs0.2167 11456 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.49 Å2 / Biso mean: 81.9806 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.983→26.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 4 0 4252
Biso mean--158.89 --
Num. residues----546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2560X-RAY DIFFRACTION8.77TORSIONAL
12B2560X-RAY DIFFRACTION8.77TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.983-3.28240.38961370.3158272998
3.2824-3.75620.33151440.2478277299
3.7562-4.72820.25751330.2022275799
4.7282-100.22131280.1852265695

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