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- PDB-4utw: Structural characterisation of NanE, ManNac6P C2 epimerase, from ... -

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Basic information

Entry
Database: PDB / ID: 4utw
TitleStructural characterisation of NanE, ManNac6P C2 epimerase, from Clostridium perfingens
Components(PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE) x 2
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-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-acetyl-D-glucosamine-6-phosphate / Putative N-acetylmannosamine-6-phosphate 2-epimerase / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS STR. 13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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. THE SHEETS PRESENTED AS "CA" 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 "DA" 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: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
D: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,89612
Polymers100,5574
Non-polymers1,3398
Water17,997999
1
A: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
D: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-56.9 kcal/mol
Surface area19350 Å2
MethodPISA
2
B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules

C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area3540 Å2
ΔGint-55.6 kcal/mol
Surface area19360 Å2
MethodPISA
3
C: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules

B: PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9486
Polymers50,2792
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3540 Å2
ΔGint-55.6 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.756, 75.584, 82.173
Angle α, β, γ (deg.)89.90, 89.91, 92.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 221
2114B1 - 221
3114C1 - 221
4114D1 - 221

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Components

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


Mass: 25164.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
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: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#2: Protein PUTATIVE N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE / MANNAC-6-P EPIMERASE / N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE


Mass: 25113.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8 CHLORIDE IONS AND 4 ACTETATE MOLECULES ARE BOUND TO THE 4 MONOMERS
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: Q0TUP9, UniProt: Q8XNZ3*PLUS, N-acylglucosamine-6-phosphate 2-epimerase
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-RFW / N-acetyl-D-glucosamine-6-phosphate


Mass: 299.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H14NO9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.37 Å3/Da / Density % sol: 48.24 % / Description: NONE
Crystal growDetails: 0.1 M NA CACODYLATE PH 6.5, 0.2 M CA ACETATE, 24.5% (W/V) PEG 2K MME AND 5% (V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→41.1 Å / Num. obs: 63357 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.5 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UTT

4utt


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.458 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24805 3129 4.9 %RANDOM
Rwork0.18515 ---
obs0.18832 60227 90.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.44 Å20.23 Å2
2---0.47 Å2-0.03 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 80 999 8107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227353
X-RAY DIFFRACTIONr_bond_other_d0.0010.024963
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9879966
X-RAY DIFFRACTIONr_angle_other_deg1.005312300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26725.216301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.619151394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5051537
X-RAY DIFFRACTIONr_chiral_restr0.0990.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.54625
X-RAY DIFFRACTIONr_mcbond_other0.2421.51887
X-RAY DIFFRACTIONr_mcangle_it1.07627513
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9432728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8964.52430
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 2695 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.330.5
2Bmedium positional0.320.5
3Cmedium positional0.380.5
4Dmedium positional0.380.5
1Amedium thermal0.692
2Bmedium thermal0.712
3Cmedium thermal0.662
4Dmedium thermal0.72
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 212 -
Rwork0.245 4219 -
obs--85.67 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0658-0.04360.07031.16630.1570.88930.01830.0707-0.1002-0.036-0.02530.04120.0787-0.04410.0070.0114-0.0077-0.00120.0202-0.00990.011-5.5589-2.8718-41.151
21.0353-0.036-0.05231.1608-0.14690.79280.01160.07130.1139-0.0412-0.0233-0.035-0.07220.03930.01170.0096-0.00440.0010.01730.00910.0136-0.7133-1.176-0.0141
30.76560.1281-0.04611.1123-0.18330.67-0.003-0.0214-0.16990.0043-0.01580.08480.1179-0.0280.01880.0271-0.0145-0.00010.0351-0.00670.0799-11.9651-34.975-71.6795
40.83640.18170.03261.2070.20760.6091-0.0075-0.01370.17850.0251-0.0124-0.0894-0.10840.04010.01990.0264-0.0145-0.00710.03160.0030.06445.503630.6648-30.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-8 - 220
2X-RAY DIFFRACTION2B-8 - 220
3X-RAY DIFFRACTION3C-8 - 220
4X-RAY DIFFRACTION4D-8 - 220

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