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- PDB-3iv8: N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae ... -

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Basic information

Entry
Database: PDB / ID: 3iv8
TitleN-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae complexed with fructose 6-phosphate
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsHYDROLASE / IDP01334 / N-acetylglucosamine-6-phosphate deacetylase / fructose 6-phosphate / Carbohydrate metabolism / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase / N-acetylgalactosamine-6-phosphate deacetylase activity / N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine catabolic process / N-acetylneuraminate catabolic process / protein homotetramerization / carbohydrate metabolic process / metal ion binding
Similarity search - Function
N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...N-acetylglucosamine-6-phosphate deacetylase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / NICKEL (II) ION / N-acetylglucosamine-6-phosphate deacetylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsOsipiuk, J. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae complexed with fructose 6-phosphate.
Authors: Osipiuk, J. / Maltseva, N. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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-acetylglucosamine-6-phosphate deacetylase
B: N-acetylglucosamine-6-phosphate deacetylase
C: N-acetylglucosamine-6-phosphate deacetylase
D: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,87112
Polymers165,0884
Non-polymers7838
Water5,981332
1
A: N-acetylglucosamine-6-phosphate deacetylase
C: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0186
Polymers82,5442
Non-polymers4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-44 kcal/mol
Surface area28400 Å2
MethodPISA
2
B: N-acetylglucosamine-6-phosphate deacetylase
D: N-acetylglucosamine-6-phosphate deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8546
Polymers82,5442
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-59 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.181, 123.047, 156.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
N-acetylglucosamine-6-phosphate deacetylase / / GlcNAc 6-P deacetylase


Mass: 41272.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: nagA, VC_0994 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O32445, N-acetylglucosamine-6-phosphate deacetylase
#2: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M di-sodium hydrogen phosphate, 20% PEG-3350, 5 mM fructose 6-phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 2, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→35.2 Å / Num. all: 54289 / Num. obs: 54289 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.111 / Χ2: 1.074 / Net I/σ(I): 6.7
Reflection shellResolution: 2.53→2.57 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.09 / Num. unique all: 2658 / Χ2: 0.827 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3EGJ

3egj


Resolution: 2.53→35.18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 24.772 / SU ML: 0.238 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.76 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2752 5.1 %RANDOM
Rwork0.183 ---
all0.186 54165 --
obs0.186 54165 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.85 Å2 / Biso mean: 34.533 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2---2.97 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.53→35.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11313 0 35 332 11680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211586
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.96515727
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49951504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.79925.553488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.709151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4081539
X-RAY DIFFRACTIONr_chiral_restr0.1030.21834
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218645
X-RAY DIFFRACTIONr_mcbond_it0.6471.57423
X-RAY DIFFRACTIONr_mcangle_it1.224211985
X-RAY DIFFRACTIONr_scbond_it2.14434163
X-RAY DIFFRACTIONr_scangle_it3.5594.53734
LS refinement shellResolution: 2.53→2.593 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 187 -
Rwork0.266 3626 -
all-3813 -
obs-3813 96.26 %
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)
10.52980.1414-0.08630.86090.03840.29940.0411-0.0046-0.03210.09790.03070.0546-0.08360.0174-0.07180.11220.00460.01640.03550.01660.0416-9.2516-8.543237.8246
20.7390.06910.06460.9671-0.18381.0840.05970.00330.00550.13270.0835-0.2554-0.02040.051-0.14320.0310.0103-0.02930.035-0.07090.148930.31457.863729.6789
30.41840.0474-0.08090.9072-0.18880.5381-0.04150.0709-0.1334-0.16020.1089-0.20490.0252-0.0399-0.06740.0736-0.02390.06880.0491-0.08070.155120.0953-17.36893.9836
40.84290.4020.30631.70310.90930.7281-0.06550.03680.1292-0.219-0.02320.1866-0.0966-0.01810.08870.07290.0025-0.02390.0278-0.01820.0515-10.296813.01959.2651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 378
2X-RAY DIFFRACTION1A500 - 702
3X-RAY DIFFRACTION1A379 - 478
4X-RAY DIFFRACTION2B0 - 378
5X-RAY DIFFRACTION2B501 - 703
6X-RAY DIFFRACTION2B379 - 456
7X-RAY DIFFRACTION3C0 - 378
8X-RAY DIFFRACTION3C501
9X-RAY DIFFRACTION3C379 - 455
10X-RAY DIFFRACTION4D0 - 378
11X-RAY DIFFRACTION4D501
12X-RAY DIFFRACTION4D379 - 455

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