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- PDB-5zli: Crystal structure of glutamine synthetase from helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 5zli
TitleCrystal structure of glutamine synthetase from helicobacter pylori
ComponentsGlutamine synthetase
KeywordsLIGASE / glutamine synthetase / enzyme / GS / helicobacter pylori / STRUCTURAL PROTEIN
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / membrane / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain ...Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsJoo, H.K. / Lee, J.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2017R1D1A1B03032109 Korea, Republic Of
710013-03-1-SB120 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2018
Title: Structural Analysis of Glutamine Synthetase from Helicobacter pylori.
Authors: Joo, H.K. / Park, Y.W. / Jang, Y.Y. / Lee, J.Y.
History
DepositionMar 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase


Theoretical massNumber of molelcules
Total (without water)327,4776
Polymers327,4776
Non-polymers00
Water00
1
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase

A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase


Theoretical massNumber of molelcules
Total (without water)654,95512
Polymers654,95512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_958-x+4,y,-z+31
Unit cell
Length a, b, c (Å)191.085, 131.462, 131.411
Angle α, β, γ (deg.)90.000, 122.670, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 10 or resseq 12 or resseq...
21(chain B and (resseq 10 or resseq 12 or resseq...
31(chain C and (resseq 10 or resseq 12 or resseq...
41(chain D and (resseq 10 or resseq 12 or resseq...
51(chain E and (resseq 10 or resseq 12 or resseq...
61(chain F and (resseq 10 or resseq 12 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 10 or resseq 12 or resseq...A10
121(chain A and (resseq 10 or resseq 12 or resseq...A12
131(chain A and (resseq 10 or resseq 12 or resseq...A15 - 16
141(chain A and (resseq 10 or resseq 12 or resseq...A0
151(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
161(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
171(chain A and (resseq 10 or resseq 12 or resseq...A127 - 1
181(chain A and (resseq 10 or resseq 12 or resseq...A177 - 17
191(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
1101(chain A and (resseq 10 or resseq 12 or resseq...A181 - 185
1111(chain A and (resseq 10 or resseq 12 or resseq...A187 - 207
1121(chain A and (resseq 10 or resseq 12 or resseq...A209 - 211
1131(chain A and (resseq 10 or resseq 12 or resseq...A219 - 233
1141(chain A and (resseq 10 or resseq 12 or resseq...A235 - 287
1151(chain A and (resseq 10 or resseq 12 or resseq...A303 - 3
1161(chain A and (resseq 10 or resseq 12 or resseq...A8 - 481
1171(chain A and (resseq 10 or resseq 12 or resseq...A366 - 399
1181(chain A and (resseq 10 or resseq 12 or resseq...A411 - 41
1191(chain A and (resseq 10 or resseq 12 or resseq...A421 - 427
1201(chain A and (resseq 10 or resseq 12 or resseq...A421 - 427
1211(chain A and (resseq 10 or resseq 12 or resseq...A429 - 443
1221(chain A and (resseq 10 or resseq 12 or resseq...A445 - 448
1231(chain A and (resseq 10 or resseq 12 or resseq...A450 - 481
211(chain B and (resseq 10 or resseq 12 or resseq...B10
221(chain B and (resseq 10 or resseq 12 or resseq...B12
231(chain B and (resseq 10 or resseq 12 or resseq...B15 - 16
241(chain B and (resseq 10 or resseq 12 or resseq...B18 - 53
251(chain B and (resseq 10 or resseq 12 or resseq...B0
261(chain B and (resseq 10 or resseq 12 or resseq...B7 - 481
271(chain B and (resseq 10 or resseq 12 or resseq...B165 - 166
281(chain B and (resseq 10 or resseq 12 or resseq...B177 - 179
291(chain B and (resseq 10 or resseq 12 or resseq...B7 - 481
2101(chain B and (resseq 10 or resseq 12 or resseq...B187 - 207
2111(chain B and (resseq 10 or resseq 12 or resseq...B209 - 211
2121(chain B and (resseq 10 or resseq 12 or resseq...B217
2131(chain B and (resseq 10 or resseq 12 or resseq...B2119 - 2
2141(chain B and (resseq 10 or resseq 12 or resseq...B290 - 301
2151(chain B and (resseq 10 or resseq 12 or resseq...B303 - 360
2161(chain B and (resseq 10 or resseq 12 or resseq...B303 - 360
2171(chain B and (resseq 10 or resseq 12 or resseq...B401 - 409
2181(chain B and (resseq 10 or resseq 12 or resseq...B411 - 419
2191(chain B and (resseq 10 or resseq 12 or resseq...B421 - 424
2201(chain B and (resseq 10 or resseq 12 or resseq...B416 - 417
2211(chain B and (resseq 10 or resseq 12 or resseq...B429 - 447
2221(chain B and (resseq 10 or resseq 12 or resseq...B445 - 443
2231(chain B and (resseq 10 or resseq 12 or resseq...B445 - 448
2241(chain B and (resseq 10 or resseq 12 or resseq...B450 - 481
311(chain C and (resseq 10 or resseq 12 or resseq...C10
321(chain C and (resseq 10 or resseq 12 or resseq...C12
331(chain C and (resseq 10 or resseq 12 or resseq...C15 - 16
341(chain C and (resseq 10 or resseq 12 or resseq...C184 - 125
351(chain C and (resseq 10 or resseq 12 or resseq...C124 - 12163
361(chain C and (resseq 10 or resseq 12 or resseq...C165 - 166
371(chain C and (resseq 10 or resseq 12 or resseq...C168 - 174
381(chain C and (resseq 10 or resseq 12 or resseq...C177 - 179
391(chain C and (resseq 10 or resseq 12 or resseq...C181 - 185
3101(chain C and (resseq 10 or resseq 12 or resseq...C187 - 207
3111(chain C and (resseq 10 or resseq 12 or resseq...C209 - 21
3121(chain C and (resseq 10 or resseq 12 or resseq...C217
3131(chain C and (resseq 10 or resseq 12 or resseq...C219 - 233
3141(chain C and (resseq 10 or resseq 12 or resseq...C235 - 287
3151(chain C and (resseq 10 or resseq 12 or resseq...C303 - 360
3161(chain C and (resseq 10 or resseq 12 or resseq...C362 - 36
3171(chain C and (resseq 10 or resseq 12 or resseq...C366 - 399
3181(chain C and (resseq 10 or resseq 12 or resseq...C401 - 409
3191(chain C and (resseq 10 or resseq 12 or resseq...C411 - 414
3201(chain C and (resseq 10 or resseq 12 or resseq...C416 - 417
3211(chain C and (resseq 10 or resseq 12 or resseq...C421 - 427
3221(chain C and (resseq 10 or resseq 12 or resseq...C429 - 443
3231(chain C and (resseq 10 or resseq 12 or resseq...C445 - 448
3241(chain C and (resseq 10 or resseq 12 or resseq...C450 - 481
411(chain D and (resseq 10 or resseq 12 or resseq...D10
421(chain D and (resseq 10 or resseq 12 or resseq...D12
431(chain D and (resseq 10 or resseq 12 or resseq...D15 - 16
441(chain D and (resseq 10 or resseq 12 or resseq...D184 - 125
451(chain D and (resseq 10 or resseq 12 or resseq...D124 - 12163
461(chain D and (resseq 10 or resseq 12 or resseq...D165 - 166
471(chain D and (resseq 10 or resseq 12 or resseq...D168 - 174
481(chain D and (resseq 10 or resseq 12 or resseq...D177 - 179
491(chain D and (resseq 10 or resseq 12 or resseq...D181 - 185
4101(chain D and (resseq 10 or resseq 12 or resseq...D187 - 207
4111(chain D and (resseq 10 or resseq 12 or resseq...D209 - 21
4121(chain D and (resseq 10 or resseq 12 or resseq...D217
4131(chain D and (resseq 10 or resseq 12 or resseq...D219 - 233
4141(chain D and (resseq 10 or resseq 12 or resseq...D235 - 287
4151(chain D and (resseq 10 or resseq 12 or resseq...D303 - 360
4161(chain D and (resseq 10 or resseq 12 or resseq...D362 - 36
4171(chain D and (resseq 10 or resseq 12 or resseq...D366 - 399
4181(chain D and (resseq 10 or resseq 12 or resseq...D401 - 409
4191(chain D and (resseq 10 or resseq 12 or resseq...D411 - 414
4201(chain D and (resseq 10 or resseq 12 or resseq...D416 - 417
4211(chain D and (resseq 10 or resseq 12 or resseq...D421 - 427
4221(chain D and (resseq 10 or resseq 12 or resseq...D429 - 443
4231(chain D and (resseq 10 or resseq 12 or resseq...D445 - 448
4241(chain D and (resseq 10 or resseq 12 or resseq...D450 - 481
511(chain E and (resseq 10 or resseq 12 or resseq...E10
521(chain E and (resseq 10 or resseq 12 or resseq...E12
531(chain E and (resseq 10 or resseq 12 or resseq...E15 - 16
541(chain E and (resseq 10 or resseq 12 or resseq...E18 - 53
551(chain E and (resseq 10 or resseq 12 or resseq...E0
561(chain E and (resseq 10 or resseq 12 or resseq...E8 - 481
571(chain E and (resseq 10 or resseq 12 or resseq...E165 - 166
581(chain E and (resseq 10 or resseq 12 or resseq...E177 - 179
591(chain E and (resseq 10 or resseq 12 or resseq...E8 - 481
5101(chain E and (resseq 10 or resseq 12 or resseq...E187 - 207
5111(chain E and (resseq 10 or resseq 12 or resseq...E209 - 211
5121(chain E and (resseq 10 or resseq 12 or resseq...E217
5131(chain E and (resseq 10 or resseq 12 or resseq...E2119 - 2
5141(chain E and (resseq 10 or resseq 12 or resseq...E290 - 301
5151(chain E and (resseq 10 or resseq 12 or resseq...E303 - 360
5161(chain E and (resseq 10 or resseq 12 or resseq...E303 - 360
5171(chain E and (resseq 10 or resseq 12 or resseq...E401 - 409
5181(chain E and (resseq 10 or resseq 12 or resseq...E411 - 419
5191(chain E and (resseq 10 or resseq 12 or resseq...E421 - 424
5201(chain E and (resseq 10 or resseq 12 or resseq...E416 - 417
5211(chain E and (resseq 10 or resseq 12 or resseq...E429 - 447
5221(chain E and (resseq 10 or resseq 12 or resseq...E445 - 443
5231(chain E and (resseq 10 or resseq 12 or resseq...E445 - 448
5241(chain E and (resseq 10 or resseq 12 or resseq...E450 - 481
611(chain F and (resseq 10 or resseq 12 or resseq...F10
621(chain F and (resseq 10 or resseq 12 or resseq...F12
631(chain F and (resseq 10 or resseq 12 or resseq...F15 - 16
641(chain F and (resseq 10 or resseq 12 or resseq...F184 - 125
651(chain F and (resseq 10 or resseq 12 or resseq...F124 - 12163
661(chain F and (resseq 10 or resseq 12 or resseq...F165 - 166
671(chain F and (resseq 10 or resseq 12 or resseq...F168 - 174
681(chain F and (resseq 10 or resseq 12 or resseq...F177 - 179
691(chain F and (resseq 10 or resseq 12 or resseq...F181 - 185
6101(chain F and (resseq 10 or resseq 12 or resseq...F187 - 207
6111(chain F and (resseq 10 or resseq 12 or resseq...F209 - 21
6121(chain F and (resseq 10 or resseq 12 or resseq...F217
6131(chain F and (resseq 10 or resseq 12 or resseq...F219 - 233
6141(chain F and (resseq 10 or resseq 12 or resseq...F235 - 287
6151(chain F and (resseq 10 or resseq 12 or resseq...F303 - 360
6161(chain F and (resseq 10 or resseq 12 or resseq...F362 - 36
6171(chain F and (resseq 10 or resseq 12 or resseq...F366 - 399
6181(chain F and (resseq 10 or resseq 12 or resseq...F401 - 409
6191(chain F and (resseq 10 or resseq 12 or resseq...F411 - 414
6201(chain F and (resseq 10 or resseq 12 or resseq...F416 - 417
6211(chain F and (resseq 10 or resseq 12 or resseq...F421 - 427
6221(chain F and (resseq 10 or resseq 12 or resseq...F429 - 443
6231(chain F and (resseq 10 or resseq 12 or resseq...F445 - 448
6241(chain F and (resseq 10 or resseq 12 or resseq...F450 - 481

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Components

#1: Protein
Glutamine synthetase / GS / Glutamate--ammonia ligase / Glutamine synthetase I beta / GSI beta


Mass: 54579.543 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: glnA, HP_0512 / Production host: Escherichia coli (E. coli) / References: UniProt: P94845, glutamine synthetase

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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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 6000, choline, Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 67460 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.19 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.076 / Rrim(I) all: 0.14 / Χ2: 1.085 / Net I/σ(I): 7 / Num. measured all: 224008
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.853.40.43133640.7580.2760.5130.81299.8
2.85-2.93.40.38133430.80.2440.4530.88599.4
2.9-2.963.30.34933680.8170.2250.4160.92999.8
2.96-3.023.30.31433310.8580.2040.3750.92799.6
3.02-3.083.10.26833860.8750.1810.3251.11799.7
3.08-3.153.20.25833730.8940.1710.311.1399.8
3.15-3.233.40.2433900.9050.1540.2861.05299.6
3.23-3.323.50.21133400.9290.1330.251.13799.9
3.32-3.423.50.18733780.9450.1190.2221.19399.6
3.42-3.533.40.17233630.9470.110.2041.18999.7
3.53-3.653.40.1533780.9550.0960.1791.22399.5
3.65-3.83.30.12933450.9690.0840.1541.18399.5
3.8-3.973.20.11833800.9740.0780.1411.3599.2
3.97-4.1830.10133370.9760.070.1231.23799.3
4.18-4.443.40.09433860.9780.060.1121.12799.6
4.44-4.793.40.0933650.980.0580.1071.08899.3
4.79-5.273.40.08434200.9830.0550.1011.00499.6
5.27-6.033.10.08433800.9810.0560.1011.03699.8
6.03-7.593.40.07633990.9880.0480.0910.98299.6
7.59-503.30.06234340.9910.040.0741.13198.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 2.8→19.996 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2601 1982 2.97 %
Rwork0.1899 --
obs0.192 66840 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.6 Å2 / Biso mean: 43.9134 Å2 / Biso min: 14.38 Å2
Refinement stepCycle: final / Resolution: 2.8→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22540 0 0 0 22540
Num. residues----2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123140
X-RAY DIFFRACTIONf_angle_d1.27831283
X-RAY DIFFRACTIONf_chiral_restr0.0683260
X-RAY DIFFRACTIONf_plane_restr0.0094103
X-RAY DIFFRACTIONf_dihedral_angle_d18.11813665
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12079X-RAY DIFFRACTION12.586TORSIONAL
12B12079X-RAY DIFFRACTION12.586TORSIONAL
13C12079X-RAY DIFFRACTION12.586TORSIONAL
14D12079X-RAY DIFFRACTION12.586TORSIONAL
15E12079X-RAY DIFFRACTION12.586TORSIONAL
16F12079X-RAY DIFFRACTION12.586TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.86990.32351400.205146014741100
2.8699-2.94730.32191420.208346224764100
2.9473-3.03370.26371410.21546104751100
3.0337-3.13130.32481430.21646684811100
3.1313-3.24270.31481390.218945474686100
3.2427-3.3720.29911420.214846734815100
3.372-3.52460.28811410.206446094750100
3.5246-3.70940.26881410.202346184759100
3.7094-3.94010.27061410.20194595473699
3.9401-4.24170.27571410.19634649479099
4.2417-4.66360.23561430.18446544797100
4.6636-5.32730.25161410.180546304771100
5.3273-6.67010.2591430.187446744817100
6.6701-19.99640.16941440.13544708485299

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