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- PDB-7lqn: Glucosamine-6-phosphate Deaminase from H. influenzae -

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Basic information

Entry
Database: PDB / ID: 7lqn
TitleGlucosamine-6-phosphate Deaminase from H. influenzae
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSubramanian, R. / Srinivasachari, S.
Funding support India, United Kingdom, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/IN/Sweden/06/SR/2017-18 India
Wellcome Trust500210-Z-11-Z United Kingdom
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: Author supporting evidence / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / 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 / _pdbx_audit_support.country / _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

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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
E: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase
G: Glucosamine-6-phosphate deaminase
H: Glucosamine-6-phosphate deaminase
I: Glucosamine-6-phosphate deaminase
J: Glucosamine-6-phosphate deaminase
K: Glucosamine-6-phosphate deaminase
L: Glucosamine-6-phosphate deaminase


Theoretical massNumber of molelcules
Total (without water)389,51712
Polymers389,51712
Non-polymers00
Water00
1
A: Glucosamine-6-phosphate deaminase
B: Glucosamine-6-phosphate deaminase
C: Glucosamine-6-phosphate deaminase
D: Glucosamine-6-phosphate deaminase
E: Glucosamine-6-phosphate deaminase
F: Glucosamine-6-phosphate deaminase


Theoretical massNumber of molelcules
Total (without water)194,7586
Polymers194,7586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Glucosamine-6-phosphate deaminase
H: Glucosamine-6-phosphate deaminase
I: Glucosamine-6-phosphate deaminase
J: Glucosamine-6-phosphate deaminase
K: Glucosamine-6-phosphate deaminase
L: Glucosamine-6-phosphate deaminase


Theoretical massNumber of molelcules
Total (without water)194,7586
Polymers194,7586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.405, 144.300, 131.143
Angle α, β, γ (deg.)90.000, 92.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J
111chain K
121chain L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 0 - 260 / Label seq-ID: 16 - 276

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF
7chain GGG
8chain HHH
9chain III
10chain JJJ
11chain KKK
12chain LLL

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Components

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


Mass: 32459.719 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain 86-028NP) (bacteria)
Strain: 86-028NP / Gene: nagB, NTHI0227 / Plasmid: pET300/NT-DEST / Details (production host): Gateway cloning / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Bl21(De3)*
References: UniProt: Q4QP46, glucosamine-6-phosphate deaminase

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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: 2.35 Å3/Da / Density % sol: 51 % / Description: Cuboid
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2 % w/v Tasciminate pH 5.0, 0.1 M Sodium Citrate tribasic pH 5.6, 16 % PEG 3350 with 0.1 M Strontium Chloride. 6H2O as additive

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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: 3→48.67 Å / Num. obs: 76608 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 46.11 Å2 / CC1/2: 0.972 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.109 / Rrim(I) all: 0.203 / Net I/σ(I): 6.4 / Num. measured all: 256858 / Scaling rejects: 202
Reflection shellResolution: 3→3.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.53 / Num. unique obs: 4516 / CC1/2: 0.845 / Rpim(I) all: 0.336 / Rrim(I) all: 0.629 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018data reduction
Aimless0.6.3data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
PHENIX1.19phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dea

1dea


Resolution: 3→47.49 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 3814 4.98 %
Rwork0.1935 72705 -
obs0.1959 76519 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.96 Å2 / Biso mean: 45.5616 Å2 / Biso min: 16.69 Å2
Refinement stepCycle: final / Resolution: 3→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25020 0 0 0 25020
Num. residues----3132
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9444X-RAY DIFFRACTION4.037TORSIONAL
12B9444X-RAY DIFFRACTION4.037TORSIONAL
13C9444X-RAY DIFFRACTION4.037TORSIONAL
14D9444X-RAY DIFFRACTION4.037TORSIONAL
15E9444X-RAY DIFFRACTION4.037TORSIONAL
16F9444X-RAY DIFFRACTION4.037TORSIONAL
17G9444X-RAY DIFFRACTION4.037TORSIONAL
18H9444X-RAY DIFFRACTION4.037TORSIONAL
19I9444X-RAY DIFFRACTION4.037TORSIONAL
110J9444X-RAY DIFFRACTION4.037TORSIONAL
111K9444X-RAY DIFFRACTION4.037TORSIONAL
112L9444X-RAY DIFFRACTION4.037TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.040.34471270.278427152842100
3.04-3.080.31721450.27072655280099
3.08-3.120.33551400.27012673281399
3.12-3.160.31941430.26692658280199
3.16-3.210.30031430.26782657280099
3.21-3.260.37931300.27972686281699
3.26-3.320.34991370.28772660279799
3.32-3.370.34961370.26372663280099
3.37-3.430.29891430.25382666280999
3.43-3.50.28721410.21682672281399
3.5-3.570.27711610.212326932854100
3.57-3.650.27471620.211226912853100
3.65-3.730.26811410.190826742815100
3.73-3.830.21491500.181326912841100
3.83-3.930.22221430.180926932836100
3.93-4.050.23081380.166827162854100
4.05-4.180.21571390.165526742813100
4.18-4.330.20511390.165427522891100
4.33-4.50.19111430.163126862829100
4.5-4.70.21361470.159227062853100
4.7-4.950.1891110.147527362847100
4.95-5.260.20541160.162627282844100
5.26-5.670.21351710.162226732844100
5.67-6.240.21581290.173227492878100
6.24-7.140.22281670.180826892856100
7.14-8.980.20071470.164427332880100
8.98-47.490.17271240.16452716284097
Refinement TLS params.Method: refined / Origin x: 125.5328 Å / Origin y: -26.5328 Å / Origin z: 98.8387 Å
111213212223313233
T0.2088 Å2-0 Å2-0.0056 Å2-0.2043 Å20.0272 Å2--0.2205 Å2
L0.0531 °2-0.0023 °2-0.0143 °2-0.0309 °20.0357 °2--0.0517 °2
S-0.0132 Å °-0.0011 Å °0.0117 Å °-0.0046 Å °0.0084 Å °-0.0008 Å °0.0024 Å °0.005 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 260
2X-RAY DIFFRACTION1allB0 - 260
3X-RAY DIFFRACTION1allC0 - 260
4X-RAY DIFFRACTION1allD0 - 260
5X-RAY DIFFRACTION1allE0 - 260
6X-RAY DIFFRACTION1allF0 - 260
7X-RAY DIFFRACTION1allG0 - 260
8X-RAY DIFFRACTION1allH0 - 260
9X-RAY DIFFRACTION1allI0 - 260
10X-RAY DIFFRACTION1allJ0 - 260
11X-RAY DIFFRACTION1allK0 - 260
12X-RAY DIFFRACTION1allL0 - 260

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