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- PDB-5zjp: Structure of N-acetylmannosamine-6-phosphate-2-epimerase from Vib... -

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Basic information

Entry
Database: PDB / ID: 5zjp
TitleStructure of N-acetylmannosamine-6-phosphate-2-epimerase from Vibrio cholerae with N-acetylglucosamine-6-phosphate
ComponentsPutative N-acetylmannosamine-6-phosphate 2-epimerase
KeywordsISOMERASE / Sialic acid Catabolism Pathway
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-acetyl-D-glucosamine-6-phosphate / : / Putative N-acetylmannosamine-6-phosphate 2-epimerase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsManjunath, L. / Guntupalli, S.R.
Funding support India, 1items
OrganizationGrant numberCountry
BT/IN/SWEDEN/41/SR/2013 India
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures and kinetic analyses of N-acetylmannosamine-6-phosphate 2-epimerases from Fusobacterium nucleatum and Vibrio cholerae
Authors: Manjunath, L. / Guntupalli, S.R. / Currie, M.J. / North, R.A. / Dobson, R.C.J. / Nayak, V. / Subramanian, R.
History
DepositionMar 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative N-acetylmannosamine-6-phosphate 2-epimerase
B: Putative N-acetylmannosamine-6-phosphate 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6248
Polymers48,6012
Non-polymers1,0236
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-22 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.959, 70.653, 149.362
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 7:32 or resseq 34:35 or resseq...
21(chain B and (resseq 7:32 or resseq 34:35 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 7:32 or resseq 34:35 or resseq...A7 - 32
121(chain A and (resseq 7:32 or resseq 34:35 or resseq...A34 - 35
131(chain A and (resseq 7:32 or resseq 34:35 or resseq...A37 - 118
141(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
151(chain A and (resseq 7:32 or resseq 34:35 or resseq...A165 - 170
161(chain A and (resseq 7:32 or resseq 34:35 or resseq...A172 - 177
171(chain A and (resseq 7:32 or resseq 34:35 or resseq...A1
181(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
191(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
1101(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
1111(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
1121(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
1131(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
1141(chain A and (resseq 7:32 or resseq 34:35 or resseq...A5 - 231
211(chain B and (resseq 7:32 or resseq 34:35 or resseq...B7 - 32
221(chain B and (resseq 7:32 or resseq 34:35 or resseq...B34 - 35
231(chain B and (resseq 7:32 or resseq 34:35 or resseq...B138
241(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
251(chain B and (resseq 7:32 or resseq 34:35 or resseq...B165 - 170
261(chain B and (resseq 7:32 or resseq 34:35 or resseq...B17272 - 177
271(chain B and (resseq 7:32 or resseq 34:35 or resseq...B179
281(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
291(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2101(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2111(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2121(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2131(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2141(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232
2151(chain B and (resseq 7:32 or resseq 34:35 or resseq...B3 - 232

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative N-acetylmannosamine-6-phosphate 2-epimerase / ManNAc-6-P epimerase


Mass: 24300.412 Da / Num. of mol.: 2 / Fragment: UNP residues 7-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: nanE / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K2UT85, UniProt: Q9KR62*PLUS, N-acylglucosamine-6-phosphate 2-epimerase

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Non-polymers , 5 types, 10 molecules

#2: Chemical ChemComp-RFW / N-acetyl-D-glucosamine-6-phosphate


Mass: 299.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14NO9P
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M Malonate, pH 5.0, 20% PEG 3350, 1M Malonate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.66→49.79 Å / Num. obs: 15416 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 43.02 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.062 / Rrim(I) all: 0.152 / Net I/σ(I): 8.7 / Num. measured all: 89562 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.66-2.795.30.4931002219000.8920.230.5452.494.3
8.82-49.795.20.05726134990.9950.0270.06418.899.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→40.945 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 736 4.79 %
Rwork0.2304 14623 -
obs0.2326 15359 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.76 Å2 / Biso mean: 45.4206 Å2 / Biso min: 22.93 Å2
Refinement stepCycle: final / Resolution: 2.66→40.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 66 4 3429
Biso mean--51.85 41.35 -
Num. residues----453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043472
X-RAY DIFFRACTIONf_angle_d0.7714715
X-RAY DIFFRACTIONf_chiral_restr0.047567
X-RAY DIFFRACTIONf_plane_restr0.005611
X-RAY DIFFRACTIONf_dihedral_angle_d12.7062062
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1860X-RAY DIFFRACTION5.935TORSIONAL
12B1860X-RAY DIFFRACTION5.935TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.66-2.86540.34721510.29162787293896
2.8654-3.15360.33361280.25792875300399
3.1536-3.60970.23821630.244129053068100
3.6097-4.54690.2881410.213929633104100
4.5469-40.94960.24751530.211130933246100

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