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- PDB-6jku: Crystal structure of N-acetylglucosamine-6-phosphate deacetylase ... -

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Basic information

Entry
Database: PDB / ID: 6jku
TitleCrystal structure of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella Multocida
ComponentsN-acetylglucosamine-6-phosphate deacetylase
KeywordsMETAL BINDING PROTEIN / deacetylase / sialic acid catabolism pathway
Function / homology
Function and homology information


N-acetylglucosamine-6-phosphate deacetylase activity / N-acetylglucosamine metabolic process / 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
PHOSPHATE ION / N-acetylglucosamine-6-phosphate deacetylase / NagA
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsManjunath, L. / Bose, S. / Subramanian, R.
Funding support India, 4items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/INF/22/SP22660/2017 India
Department of Biotechnology (India)BT/PR12422/MED /31/287/214 India
Department of Biotechnology (India)BT/PR5081/INF/156/2012 India
Department of Biotechnology (India)BT/IN/SWEDEN/06/SR/2017-2018 India
CitationJournal: Proteins / Year: 2020
Title: Quaternary variations in the structural assembly of N-acetylglucosamine-6-phosphate deacetylase from Pasteurella multocida.
Authors: Manjunath, L. / Coombes, D. / Davies, J. / Dhurandhar, M. / Tiwari, V.R. / Dobson, R.C.J. / Sowdhamini, R. / Ramaswamy, S. / Bose, S.
History
DepositionMar 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 17, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Nov 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-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)174,91551
Polymers171,5874
Non-polymers3,32847
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Cryo electron microscopy was also performed
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-258 kcal/mol
Surface area51550 Å2
Unit cell
Length a, b, c (Å)89.162, 139.549, 166.556
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
N-acetylglucosamine-6-phosphate deacetylase


Mass: 42896.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (bacteria) / Strain: Pm70 / Gene: BGK37_09560 / Plasmid: pET300 NT/DEST / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1E3XI56, UniProt: Q9CMF5*PLUS

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Non-polymers , 6 types, 1200 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium salt pH 7.5, 0.8 M Sodium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.95→47.13 Å / Num. obs: 134675 / % possible obs: 89.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 13.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.052 / Rrim(I) all: 0.124 / Net I/σ(I): 10
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6848 / CC1/2: 0.636 / Rpim(I) all: 0.526 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P50

2p50


Resolution: 1.95→47.129 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 6601 4.9 %
Rwork0.1632 128029 -
obs0.165 134630 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 27.3031 Å2 / Biso min: 12.44 Å2
Refinement stepCycle: final / Resolution: 1.95→47.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11432 0 183 1154 12769
Biso mean--41.08 34.24 -
Num. residues----1528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97220.27792260.24674368459492
1.9722-1.99540.26822240.22824388461292
1.9954-2.01970.29322190.23324468468794
2.0197-2.04530.25962080.2274430463893
2.0453-2.07220.26782310.2124444467593
2.0722-2.10060.27312120.20884408462093
2.1006-2.13060.24672390.20144392463192
2.1306-2.16240.26511990.19844398459792
2.1624-2.19620.25582090.19954377458691
2.1962-2.23220.25752250.19574364458991
2.2322-2.27070.21552280.19454273450190
2.2707-2.31190.24752380.19174240447890
2.3119-2.35640.2332680.18524234450289
2.3564-2.40450.2392080.18084293450190
2.4045-2.45680.22852080.18294161436987
2.4568-2.51390.24532090.18214146435587
2.5139-2.57680.24292180.17684079429786
2.5768-2.64650.23632080.17654046425484
2.6465-2.72430.20781960.17774060425685
2.7243-2.81230.23332300.17824032426285
2.8123-2.91280.23651910.18093966415782
2.9128-3.02940.21431890.16923904409381
3.0294-3.16720.20411960.16373988418483
3.1672-3.33410.20042110.15774114432585
3.3341-3.5430.16212380.14764294453289
3.543-3.81640.15062240.13224470469492
3.8164-4.20030.15492500.12214443469391
4.2003-4.80750.13872310.11014401463290
4.8075-6.0550.15672370.1324426466390
6.055-47.14270.16372310.15254422465386

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