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- PDB-5h1w: Crystal Structure of Hyperthermophilic Thermotoga maritima L-Keto... -

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Basic information

Entry
Database: PDB / ID: 5h1w
TitleCrystal Structure of Hyperthermophilic Thermotoga maritima L-Ketose-3-Epimerase with Mn2+ and L(+)-Erythrulose
ComponentsUncharacterized protein TM_0416
KeywordsISOMERASE / epimerase / Mn2+ / hyperthermophilic / eubacterium / Erythrulose
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / inositol metabolic process / isomerase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-Erythrulose / : / 5-keto-L-gluconate epimerase
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.631 Å
AuthorsCao, T.P. / Shin, S.M. / Lee, D.W. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation2013R1A1A2057465 Korea, Republic Of
National Research Foundation2014R1A2A2A01006765 Korea, Republic Of
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C5and C6Epimerization Reactions
Authors: Shin, S.M. / Cao, T.P. / Choi, J.M. / Kim, S.B. / Lee, S.J. / Lee, S.H. / Lee, D.W.
History
DepositionOct 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein TM_0416
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4209
Polymers65,3552
Non-polymers1,0657
Water9,566531
1
A: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3295
Polymers32,6771
Non-polymers6524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint0 kcal/mol
Surface area11970 Å2
MethodPISA
2
B: Uncharacterized protein TM_0416
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0914
Polymers32,6771
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.238, 55.411, 59.004
Angle α, β, γ (deg.)107.48, 102.14, 91.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein TM_0416


Mass: 32677.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / Gene: TM_0416 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9WYP7
#2: Sugar ChemComp-LER / L-Erythrulose / (3S)-1,3,4-trihydroxybutan-2-one / Erythrulose


Type: L-saccharide / Mass: 120.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 5%(w/w) PEG1000, 20%(v/v) PEG200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2016
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 70454 / % possible obs: 95.6 % / Redundancy: 3.9 % / Net I/σ(I): 37.01
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7.46 / % possible all: 74.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JTX

5jtx
PDB Unreleased entry


Resolution: 1.631→24.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 17.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 3482 4.94 %
Rwork0.1607 --
obs0.1617 70450 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.631→24.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4287 0 66 531 4884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094458
X-RAY DIFFRACTIONf_angle_d1.2645969
X-RAY DIFFRACTIONf_dihedral_angle_d15.1791689
X-RAY DIFFRACTIONf_chiral_restr0.049669
X-RAY DIFFRACTIONf_plane_restr0.005762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6305-1.65280.2081910.19572037X-RAY DIFFRACTION73
1.6528-1.67640.23281460.20322555X-RAY DIFFRACTION90
1.6764-1.70150.25351370.19772603X-RAY DIFFRACTION96
1.7015-1.7280.22811460.18682739X-RAY DIFFRACTION96
1.728-1.75640.23741530.18472649X-RAY DIFFRACTION96
1.7564-1.78660.24391570.17632701X-RAY DIFFRACTION96
1.7866-1.81910.20571340.1692633X-RAY DIFFRACTION96
1.8191-1.85410.18221320.16592736X-RAY DIFFRACTION96
1.8541-1.89190.19821510.16162697X-RAY DIFFRACTION97
1.8919-1.9330.16291410.15952712X-RAY DIFFRACTION97
1.933-1.9780.19441530.1562684X-RAY DIFFRACTION97
1.978-2.02740.17171400.15562700X-RAY DIFFRACTION97
2.0274-2.08220.17711430.15262715X-RAY DIFFRACTION97
2.0822-2.14350.17591380.1542722X-RAY DIFFRACTION97
2.1435-2.21260.19311180.15322740X-RAY DIFFRACTION97
2.2126-2.29160.16771560.1552745X-RAY DIFFRACTION98
2.2916-2.38330.19021380.15162720X-RAY DIFFRACTION98
2.3833-2.49170.19341590.16622730X-RAY DIFFRACTION98
2.4917-2.62290.1911310.16752772X-RAY DIFFRACTION98
2.6229-2.7870.18821320.16582752X-RAY DIFFRACTION98
2.787-3.00190.17071270.16122769X-RAY DIFFRACTION99
3.0019-3.30330.1721310.15922783X-RAY DIFFRACTION99
3.3033-3.77980.14791360.14712761X-RAY DIFFRACTION99
3.7798-4.75640.14641350.14312701X-RAY DIFFRACTION97
4.7564-24.51320.19031570.17782612X-RAY DIFFRACTION94

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