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- PDB-7lqm: Glucosamie-6-phosphate Deaminase from Pasturella multocida -

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Basic information

Entry
Database: PDB / ID: 7lqm
TitleGlucosamie-6-phosphate Deaminase from Pasturella multocida
ComponentsGlucosamine-6-phosphate deaminase
KeywordsHYDROLASE / Deaminase / NagB / Sialic Acid
Function / homology
Function and homology information


glucosamine-6-phosphate deaminase / glucosamine-6-phosphate deaminase activity / N-acetylglucosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process
Similarity search - Function
Glucosamine-6-phosphate isomerase, conserved site / Glucosamine/galactosamine-6-phosphate isomerases signature. / Glucosamine-6-phosphate isomerase / Glucosamine/galactosamine-6-phosphate isomerase / Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase / NagB/RpiA transferase-like
Similarity search - Domain/homology
Glucosamine-6-phosphate deaminase
Similarity search - Component
Biological speciesPasteurella multocida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSubramanian, R. / Srinivasachari, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/IN/Sweden/06/SR/2017-18 India
CitationJournal: Plos One / Year: 2023
Title: A dimer between monomers and hexamers-Oligomeric variations in glucosamine-6-phosphate deaminase family.
Authors: Srinivasachari, S. / Tiwari, V.R. / Kharbanda, T. / Sowdamini, R. / Subramanian, R.
History
DepositionFeb 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5208
Polymers129,2714
Non-polymers2484
Water2,342130
1
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6983
Polymers64,6362
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8225
Polymers64,6362
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.796, 79.569, 85.295
Angle α, β, γ (deg.)90.000, 109.130, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 100 or resid 102...
21(chain B and (resid 16 through 100 or resid 102...
31(chain C and (resid 16 through 100 or resid 102...
41(chain D and (resid 16 through 100 or resid 102...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYR(chain A and (resid 16 through 100 or resid 102...AA16 - 10018 - 102
12SERSERTHRTHR(chain A and (resid 16 through 100 or resid 102...AA102 - 178104 - 180
13THRTHRASNASN(chain A and (resid 16 through 100 or resid 102...AA181 - 191183 - 193
14PROPROSERSER(chain A and (resid 16 through 100 or resid 102...AA197 - 234199 - 236
15TRPTRPHISHIS(chain A and (resid 16 through 100 or resid 102...AA239 - 247241 - 249
16ARGARGALAALA(chain A and (resid 16 through 100 or resid 102...AA249 - 277251 - 279
21METMETTYRTYR(chain B and (resid 16 through 100 or resid 102...BB16 - 10018 - 102
22SERSERTHRTHR(chain B and (resid 16 through 100 or resid 102...BB102 - 178104 - 180
23THRTHRSERSER(chain B and (resid 16 through 100 or resid 102...BB181 - 186183 - 188
24ARGARGARGARG(chain B and (resid 16 through 100 or resid 102...BB187189
25METMETLYSLYS(chain B and (resid 16 through 100 or resid 102...BB16 - 28218 - 284
26METMETLYSLYS(chain B and (resid 16 through 100 or resid 102...BB16 - 28218 - 284
27METMETLYSLYS(chain B and (resid 16 through 100 or resid 102...BB16 - 28218 - 284
28METMETLYSLYS(chain B and (resid 16 through 100 or resid 102...BB16 - 28218 - 284
31METMETTYRTYR(chain C and (resid 16 through 100 or resid 102...CC16 - 10018 - 102
32SERSERSERSER(chain C and (resid 16 through 100 or resid 102...CC102 - 186104 - 188
33ARGARGARGARG(chain C and (resid 16 through 100 or resid 102...CC187189
34METMETLYSLYS(chain C and (resid 16 through 100 or resid 102...CC16 - 28218 - 284
35METMETLYSLYS(chain C and (resid 16 through 100 or resid 102...CC16 - 28218 - 284
36METMETLYSLYS(chain C and (resid 16 through 100 or resid 102...CC16 - 28218 - 284
37METMETLYSLYS(chain C and (resid 16 through 100 or resid 102...CC16 - 28218 - 284
41METMETTYRTYR(chain D and (resid 16 through 100 or resid 102...DD16 - 10018 - 102
42SERSERTHRTHR(chain D and (resid 16 through 100 or resid 102...DD102 - 178104 - 180
43THRTHRSERSER(chain D and (resid 16 through 100 or resid 102...DD181 - 186183 - 188
44METMETLYSLYS(chain D and (resid 16 through 100 or resid 102...DD16 - 28218 - 284
45METMETLYSLYS(chain D and (resid 16 through 100 or resid 102...DD16 - 28218 - 284
46METMETLYSLYS(chain D and (resid 16 through 100 or resid 102...DD16 - 28218 - 284
47METMETLYSLYS(chain D and (resid 16 through 100 or resid 102...DD16 - 28218 - 284
48METMETLYSLYS(chain D and (resid 16 through 100 or resid 102...DD16 - 28218 - 284

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Components

#1: Protein
Glucosamine-6-phosphate deaminase / GlcN6P deaminase / GNPDA / Glucosamine-6-phosphate isomerase


Mass: 32317.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pasteurella multocida (strain Pm70) (bacteria)
Strain: Pm70 / Gene: nagB, PM0875 / Plasmid: pET300/NT-DEST / Details (production host): gateway vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): *
References: UniProt: Q9CMF4, glucosamine-6-phosphate deaminase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.16 Å3/Da / Density % sol: 41.51 % / Description: Rod Shaped crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Sodium Cacodylate/HCl pH 6.5, 200 mM Magnesium Chloride, 20 % PEG 1000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2016 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.3→41.93 Å / Num. obs: 47456 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 42.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 17.7 / Num. measured all: 156289 / Scaling rejects: 24
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
2.3-2.382.90.2031341846480.9720.1390.2474.499.5
8.91-41.9330.02125298380.9940.0150.02643.996.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSJan 26, 2018data reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dea

1dea


Resolution: 2.3→37.1 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 2277 4.8 %
Rwork0.2004 45128 -
obs0.2019 47405 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.93 Å2 / Biso mean: 58.0697 Å2 / Biso min: 28 Å2
Refinement stepCycle: final / Resolution: 2.3→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8318 0 16 130 8464
Biso mean--55.63 45.76 -
Num. residues----1047
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4728X-RAY DIFFRACTION12.235TORSIONAL
12B4728X-RAY DIFFRACTION12.235TORSIONAL
13C4728X-RAY DIFFRACTION12.235TORSIONAL
14D4728X-RAY DIFFRACTION12.235TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.350.32021370.26032829296699
2.35-2.40.27361400.23492792293299
2.4-2.460.32221460.239928112957100
2.46-2.530.28391370.23928592996100
2.53-2.610.34441380.252427862924100
2.61-2.690.2831490.251728282977100
2.69-2.790.2941520.241628222974100
2.79-2.90.30361610.243227912952100
2.9-3.030.27811060.240928922998100
3.03-3.190.2651500.25628202970100
3.19-3.390.27131530.225428162969100
3.39-3.650.24211370.2082831296899
3.65-4.020.20861370.17462813295098
4.02-4.60.17811400.15722787292798
4.6-5.790.17521470.1672802294997
5.79-37.10.18551470.16512849299697
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)
11.9719-0.05991.48852.6068-0.19533.80310.1424-0.2516-0.31130.0994-0.02540.2750.2671-0.534-0.11150.3428-0.0152-0.03020.3930.00870.357110.90518.5775.768
24.4697-0.81781.53931.6023-0.26411.4701-0.0012-0.06920.01030.16430.0791-0.04730.01620.0462-0.0780.28530.00130.00060.2848-0.02820.229835.13831.146.118
31.5498-0.06991.16933.41311.55477.2089-0.0376-0.25050.25850.9146-0.0156-0.2866-0.30970.5930.05770.6978-0.0887-0.02840.62720.02110.425341.77343.1174.186
41.83920.41150.47442.5842-0.02452.9019-0.21980.02670.0621-0.21210.11230.0931-0.01360.0280.11290.2340.00530.03390.21810.00430.360977.72536.436.262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 16:277 )A16 - 277
2X-RAY DIFFRACTION2( CHAIN B AND RESID 16:282 )B16 - 282
3X-RAY DIFFRACTION3( CHAIN C AND RESID 16:282 )C16 - 282
4X-RAY DIFFRACTION4( CHAIN D AND RESID 16:282 )D16 - 282

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