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- PDB-6jtj: Crystal structure of NagZ from Neisseria gonorrhoeae in complex w... -

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Basic information

Entry
Database: PDB / ID: 6jtj
TitleCrystal structure of NagZ from Neisseria gonorrhoeae in complex with N-acetylglucosamine
ComponentsBeta-hexosaminidase
KeywordsHYDROLASE / Neisseria gonorrhoeae / acetylglucosaminidase / peptidoglycan recycling
Function / homology
Function and homology information


beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / 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 ...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: 2.18 Å
AuthorsChen, Y.
CitationJournal: To Be Published
Title: Crystal structure of native NagZ from Neisseria gonorrhoeae in complex with N-acetylglucosamine
Authors: Chen, Y.
History
DepositionApr 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,32010
Polymers257,4356
Non-polymers8854
Water19,1321062
1
A: Beta-hexosaminidase
C: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2544
Polymers85,8122
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-hexosaminidase
F: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0333
Polymers85,8122
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Beta-hexosaminidase
E: Beta-hexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0333
Polymers85,8122
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.184, 125.307, 190.614
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: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA3 - 34739 - 383
21SERSERBB3 - 34739 - 383
12SERSERAA3 - 34739 - 383
22SERSERCC3 - 34739 - 383
13SERSERAA3 - 34739 - 383
23SERSERDD3 - 34739 - 383
14SERSERAA3 - 34739 - 383
24SERSEREE3 - 34739 - 383
15SERSERAA3 - 34739 - 383
25SERSERFF3 - 34739 - 383
16SERSERBB3 - 34739 - 383
26SERSERCC3 - 34739 - 383
17PROPROBB3 - 34839 - 384
27PROPRODD3 - 34839 - 384
18SERSERBB3 - 34739 - 383
28SERSEREE3 - 34739 - 383
19SERSERBB3 - 34739 - 383
29SERSERFF3 - 34739 - 383
110SERSERCC3 - 34739 - 383
210SERSERDD3 - 34739 - 383
111SERSERCC3 - 34739 - 383
211SERSEREE3 - 34739 - 383
112SERSERCC3 - 34739 - 383
212SERSERFF3 - 34739 - 383
113SERSERDD3 - 34739 - 383
213SERSEREE3 - 34739 - 383
114SERSERDD3 - 34739 - 383
214SERSERFF3 - 34739 - 383
115SERSEREE3 - 34739 - 383
215SERSERFF3 - 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5FA94, beta-N-acetylhexosaminidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1062 / 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: 2.37 Å3/Da / Density % sol: 48.11 % / Description: rod shaped single crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: Jan 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→104.71 Å / Num. obs: 127747 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.7
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6244 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JTI

6jti


Resolution: 2.18→104.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.4 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.201 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24395 6401 5 %RANDOM
Rwork0.21443 ---
obs0.21593 120987 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0 Å20 Å2
2--0.29 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.18→104.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15608 0 60 1062 16730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01915963
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215488
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.96521583
X-RAY DIFFRACTIONr_angle_other_deg1.238335521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06852030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06723.702732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.809152669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.34815138
X-RAY DIFFRACTIONr_chiral_restr0.1220.22401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118274
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023666
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_it2.2833.4058156
X-RAY DIFFRACTIONr_mcbond_other2.2833.4048155
X-RAY DIFFRACTIONr_mcangle_it3.6525.09510174
X-RAY DIFFRACTIONr_mcangle_other3.6525.09510175
X-RAY DIFFRACTIONr_scbond_it2.5983.7317807
X-RAY DIFFRACTIONr_scbond_other2.5983.7317808
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2715.48711410
X-RAY DIFFRACTIONr_long_range_B_refined6.47727.33718762
X-RAY DIFFRACTIONr_long_range_B_other6.42927.20818360
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)
11A210020.07
12B210020.07
21A210170.07
22C210170.07
31A208690.08
32D208690.08
41A210120.08
42E210120.08
51A208620.09
52F208620.09
61B212230.07
62C212230.07
71B212820.08
72D212820.08
81B208770.08
82E208770.08
91B209230.09
92F209230.09
101C209940.08
102D209940.08
111C211230.08
112E211230.08
121C208330.09
122F208330.09
131D208980.09
132E208980.09
141D209920.09
142F209920.09
151E210550.08
152F210550.08
LS refinement shellResolution: 2.181→2.237 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 454 -
Rwork0.285 8604 -
obs--96.71 %

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