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- PDB-4utu: Structural and biochemical characterization of the N- acetylmanno... -

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Basic information

Entry
Database: PDB / ID: 4utu
TitleStructural and biochemical characterization of the N- acetylmannosamine-6-phosphate 2-epimerase from Clostridium perfringens
ComponentsN-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
KeywordsISOMERASE / SUGAR 2-EPIMERASE / SIALIC ACID / SUGAR PHOSPHATE / ENZYME MECHANISM / CARBOHYDRATE / MUTAGENESIS / 1H NMR SPECTROSCOPY
Function / homology
Function and homology information


N-acetylmannosamine catabolic process / N-acylglucosamine-6-phosphate 2-epimerase / N-acylmannosamine-6-phosphate 2-epimerase activity / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylneuraminate catabolic process / carbohydrate metabolic process / cytosol
Similarity search - Function
Putative N-acetylmannosamine-6-phosphate epimerase / Putative N-acetylmannosamine-6-phosphate epimerase / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
N-acetylmannosamine-6-phosphate / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsPelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Functional Characterization of the Clostridium Perfringens N-Acetylmannosamine-6-Phosphate 2-Epimerase Essential for the Sialic Acid Salvage Pathway
Authors: Pelissier, M.C. / Sebban-Kreuzer, C. / Guerlesquin, F. / Brannigan, J.A. / Davies, G.J. / Bourne, Y. / Vincent, F.
History
DepositionJul 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
B: N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7856
Polymers50,1112
Non-polymers6734
Water8,971498
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-56.9 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.714, 82.147, 75.195
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE / MANNAC-6-P EPIMERASE


Mass: 25055.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-ACETYLMANNOSAMINE-6-PHOSPHATE BOUND TO MOLECULE A AND B
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q8XNZ3, N-acylglucosamine-6-phosphate 2-epimerase
#2: Chemical ChemComp-LRY / N-acetylmannosamine-6-phosphate


Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.36 Å3/Da / Density % sol: 47.92 % / Description: NONE
Crystal growDetails: 0.1 M PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE BUFFER PH 8.0 AND 25% (W/V) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.45→41.1 Å / Num. obs: 78204 / % possible obs: 99.3 % / Observed criterion σ(I): 4.3 / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.3 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UTT
Resolution: 1.45→42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.745 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LYS 221 IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.16915 1565 2 %RANDOM
Rwork0.14004 ---
obs0.14062 76612 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.602 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.49 Å2
2---0.07 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 40 498 4040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223737
X-RAY DIFFRACTIONr_bond_other_d0.0020.022527
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9885081
X-RAY DIFFRACTIONr_angle_other_deg0.98136275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4155500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75525.26154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7715712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1661519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024143
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02662
X-RAY DIFFRACTIONr_nbd_refined0.2260.2729
X-RAY DIFFRACTIONr_nbd_other0.2020.22778
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21824
X-RAY DIFFRACTIONr_nbtor_other0.0880.22002
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2359
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1341.53082
X-RAY DIFFRACTIONr_mcbond_other0.2731.5958
X-RAY DIFFRACTIONr_mcangle_it1.34623835
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.52431508
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5594.51226
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 109 -
Rwork0.183 5222 -
obs--92.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8370.32791.3080.9549-0.20810.74390.04450.1706-0.0239-0.1752-0.0963-0.13760.22260.2420.05180.0574-0.00110.00790.1221-0.00640.0894-5.4684-4.687235.4694
20.6411-0.1028-0.25560.94-0.25911.33310.02620.0878-0.0241-0.15620.03630.0840.1723-0.0847-0.06240.0196-0.0095-0.0298-0.0137-0.00210.022614.6256-8.638237.6031
30.6179-0.1623-0.28041.0965-0.05981.45560.10370.12480.1384-0.16180.01330.0979-0.1477-0.0939-0.11690.02840.014-0.0051-0.00470.03440.060814.1697.019333.8941
41.66650.55930.75651.38452.38754.2850.0861-0.01350.1261-0.14680.064-0.0397-0.30960.3004-0.15010.0243-0.04180.0090.0313-0.02410.03828.39240.230553.5091
52.6649-1.18330.49411.30360.7951.41390.0389-0.2201-0.29230.03030.0240.12790.1866-0.373-0.06290.0745-0.0144-0.00120.13780.04440.121245.5474-15.874868.3628
60.75320.0587-0.15180.7067-0.12841.46590.0013-0.1233-0.09650.03860.0428-0.00550.21340.2046-0.04410.01810.0409-0.02550.04180.0010.028425.5467-16.899264.7665
71.0576-0.0054-0.0921.1127-0.17211.57050.0545-0.3569-0.04120.25240.036-0.01150.0530.2246-0.09050.06470.0202-0.02280.1692-0.0020.001725.4666-12.200580.905
80.6123-0.10240.37090.3963-0.35391.62110.0359-0.13470.09610.11760.03370.0116-0.20270.1184-0.06960.0433-0.01960.01710.0394-0.04780.041722.78841.301467.8241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 4
2X-RAY DIFFRACTION2A5 - 92
3X-RAY DIFFRACTION3A93 - 207
4X-RAY DIFFRACTION4A208 - 220
5X-RAY DIFFRACTION5B-8 - 3
6X-RAY DIFFRACTION6B4 - 95
7X-RAY DIFFRACTION7B96 - 155
8X-RAY DIFFRACTION8B156 - 220

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