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- PDB-6jti: Crystal structure of native NagZ from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 6jti
TitleCrystal structure of native NagZ from Neisseria gonorrhoeae
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / Neisseria gonorrhoeae / acetylglucosaminidase / peptidoglycan recycling
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / cytoplasm
Similarity search - Function
Beta-hexosaminidase, bacterial / Glycoside hydrolase, family 3, active site / Glycosyl hydrolases family 3 active site. / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChen, Y.
CitationJournal: To Be Published
Title: Crystal structure of native NagZ from Neisseria gonorrhoeae
Authors: Chen, Y.
History
DepositionApr 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-hexosaminidase
B: Beta-hexosaminidase
C: Beta-hexosaminidase
D: Beta-hexosaminidase
E: Beta-hexosaminidase
F: Beta-hexosaminidase


Theoretical massNumber of molelcules
Total (without water)257,4356
Polymers257,4356
Non-polymers00
Water9,746541
1
A: Beta-hexosaminidase
C: Beta-hexosaminidase


Theoretical massNumber of molelcules
Total (without water)85,8122
Polymers85,8122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
F: Beta-hexosaminidase


Theoretical massNumber of molelcules
Total (without water)85,8122
Polymers85,8122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Beta-hexosaminidase
E: Beta-hexosaminidase


Theoretical massNumber of molelcules
Total (without water)85,8122
Polymers85,8122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.017, 124.088, 189.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALPROPROAA3 - 34839 - 384
21VALVALPROPROBB3 - 34839 - 384
12VALVALSERSERAA3 - 34739 - 383
22VALVALSERSERCC3 - 34739 - 383
13VALVALPROPROAA3 - 34839 - 384
23VALVALPROPRODD3 - 34839 - 384
14VALVALSERSERAA3 - 34739 - 383
24VALVALSERSEREE3 - 34739 - 383
15VALVALSERSERAA3 - 34739 - 383
25VALVALSERSERFF3 - 34739 - 383
16VALVALALAALABB3 - 34639 - 382
26VALVALALAALACC3 - 34639 - 382
17VALVALPROPROBB3 - 34839 - 384
27VALVALPROPRODD3 - 34839 - 384
18VALVALSERSERBB3 - 34739 - 383
28VALVALSERSEREE3 - 34739 - 383
19VALVALSERSERBB3 - 34739 - 383
29VALVALSERSERFF3 - 34739 - 383
110THRTHRALAALACC2 - 34638 - 382
210THRTHRALAALADD2 - 34638 - 382
111VALVALSERSERCC3 - 34739 - 383
211VALVALSERSEREE3 - 34739 - 383
112VALVALSERSERCC3 - 34739 - 383
212VALVALSERSERFF3 - 34739 - 383
113VALVALSERSERDD3 - 34739 - 383
213VALVALSERSEREE3 - 34739 - 383
114VALVALSERSERDD3 - 34739 - 383
214VALVALSERSERFF3 - 34739 - 383
115VALVALSERSEREE3 - 34739 - 383
215VALVALSERSERFF3 - 34739 - 383

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Beta-hexosaminidase / Beta-N-acetylhexosaminidase / N-acetyl-beta-glucosaminidase


Mass: 42905.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: nagZ, NGO0135 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5FA94, beta-N-acetylhexosaminidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.33 Å3/Da / Density % sol: 47.32 % / Description: rod shape, single crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M Sodium acetate trihydrate, 20% w/v Polyethylene glycol 3,350 pH8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→103.88 Å / Num. obs: 122838 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 19.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.656 / Num. unique obs: 8959 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000data scaling
PHENIXphasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6C

4g6c


Resolution: 2.2→103.88 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.358 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23254 6172 5 %RANDOM
Rwork0.21416 ---
obs0.2151 116558 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0 Å20 Å2
2--1.43 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.2→103.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15667 0 0 541 16208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915963
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215119
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.95721563
X-RAY DIFFRACTIONr_angle_other_deg0.988334924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25652037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46223.697733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.333152682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99615138
X-RAY DIFFRACTIONr_chiral_restr0.090.22392
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023288
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5094.0488184
X-RAY DIFFRACTIONr_mcbond_other2.5084.0488183
X-RAY DIFFRACTIONr_mcangle_it46.05810209
X-RAY DIFFRACTIONr_mcangle_other46.05810210
X-RAY DIFFRACTIONr_scbond_it2.6584.3947779
X-RAY DIFFRACTIONr_scbond_other2.6584.3947779
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4396.47311355
X-RAY DIFFRACTIONr_long_range_B_refined6.36747.38416975
X-RAY DIFFRACTIONr_long_range_B_other6.3747.37616917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A213800.07
12B213800.07
21A212020.08
22C212020.08
31A212260.09
32D212260.09
41A213900.07
42E213900.07
51A213760.08
52F213760.08
61B214140.07
62C214140.07
71B216480.08
72D216480.08
81B213400.07
82E213400.07
91B213660.07
92F213660.07
101C214240.08
102D214240.08
111C212540.08
112E212540.08
121C211740.08
122F211740.08
131D213380.09
132E213380.09
141D213780.08
142F213780.08
151E214900.07
152F214900.07
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 453 -
Rwork0.294 8488 -
obs--99.75 %

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