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- PDB-5x32: Crystal structure of D-mannose isomerase -

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Basic information

Entry
Database: PDB / ID: 5x32
TitleCrystal structure of D-mannose isomerase
ComponentsN-acylglucosamine 2-epimerase
KeywordsISOMERASE
Function / homology
Function and homology information


mannose isomerase / isomerase activity / carbohydrate metabolic process
Similarity search - Function
AGE domain / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / D-mannose isomerase
Similarity search - Component
Biological speciesMarinomonas mediterranea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.586 Å
AuthorsKato, K. / Saburi, W. / Yao, M.
CitationJournal: Biochimie / Year: 2018
Title: Biochemical and structural characterization of Marinomonas mediterranead-mannose isomerase Marme_2490 phylogenetically distant from known enzymes
Authors: Saburi, W. / Jaito, N. / Kato, K. / Tanaka, Y. / Yao, M. / Mori, H.
History
DepositionFeb 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylglucosamine 2-epimerase
B: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5214
Polymers92,3312
Non-polymers1902
Water27015
1
A: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2602
Polymers46,1661
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acylglucosamine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2602
Polymers46,1661
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.915, 100.929, 192.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein N-acylglucosamine 2-epimerase


Mass: 46165.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinomonas mediterranea (strain ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1) (bacteria)
Strain: ATCC 700492 / JCM 21426 / NBRC 103028 / MMB-1 / Gene: Marme_2490 / Production host: Escherichia coli (E. coli) / References: UniProt: F2JVT6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 3350, Sodium Potassium Phosphate, Bis Tris Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.586→50 Å / Num. obs: 30332 / % possible obs: 99.3 % / Redundancy: 7.4 % / Rsym value: 0.147 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4683 / Rsym value: 0.871 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GT5

3gt5


Resolution: 2.586→43.991 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.57
RfactorNum. reflection% reflection
Rfree0.2596 1516 5 %
Rwork0.1938 --
obs0.1971 30297 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.586→43.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 10 15 6414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096616
X-RAY DIFFRACTIONf_angle_d1.2319000
X-RAY DIFFRACTIONf_dihedral_angle_d15.1132302
X-RAY DIFFRACTIONf_chiral_restr0.052896
X-RAY DIFFRACTIONf_plane_restr0.0071144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5859-2.66940.41141270.32252427X-RAY DIFFRACTION93
2.6694-2.76480.39051360.30042577X-RAY DIFFRACTION100
2.7648-2.87540.35781380.29532611X-RAY DIFFRACTION100
2.8754-3.00630.32471370.2692604X-RAY DIFFRACTION100
3.0063-3.16470.30681370.24632602X-RAY DIFFRACTION100
3.1647-3.36290.35981380.22762616X-RAY DIFFRACTION100
3.3629-3.62250.26721390.21292640X-RAY DIFFRACTION100
3.6225-3.98680.23271370.16082615X-RAY DIFFRACTION100
3.9868-4.56320.1861400.14692648X-RAY DIFFRACTION100
4.5632-5.74710.18531400.15292672X-RAY DIFFRACTION100
5.7471-43.99780.25991470.16672769X-RAY DIFFRACTION99

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