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- PDB-7cql: Apo GmaS without ligand -

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Basic information

Entry
Database: PDB / ID: 7cql
TitleApo GmaS without ligand
ComponentsType III glutamate--ammonia ligase
KeywordsLIGASE / GMA synthetase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / nitrogen fixation
Similarity search - Function
Glutamine synthetase, type III / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Type III glutamate--ammonia ligase
Similarity search - Component
Biological speciesRhodovulum sp. 12E13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of gamma-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine.
Authors: Wang, N. / Chen, X.L. / Gao, C. / Peng, M. / Wang, P. / Zhang, N. / Li, F. / Yang, G.P. / Shen, Q.T. / Li, S. / Chen, Y. / Zhang, Y.Z. / Li, C.Y.
History
DepositionAug 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase


Theoretical massNumber of molelcules
Total (without water)146,5923
Polymers146,5923
Non-polymers00
Water0
1
A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase

A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase

A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase

A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase


Theoretical massNumber of molelcules
Total (without water)586,37012
Polymers586,37012
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area54330 Å2
ΔGint-167 kcal/mol
Surface area171580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.909, 179.024, 192.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Type III glutamate--ammonia ligase


Mass: 48864.160 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodovulum sp. 12E13 (bacteria) / Gene: glnT, DLJ49_05815 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A369R1N0, 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES (pH 6.5), 1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 48331 / % possible obs: 98.6 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.04 / Rrim(I) all: 0.134 / Χ2: 7.891 / Net I/σ(I): 15.4 / Num. measured all: 545098
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.910.70.3147820.9850.0990.3252.61499.1
2.9-3.0212.40.27648280.9830.0810.2893.48799.7
3.02-3.1512.40.23648280.9880.0710.2474.77199.6
3.15-3.32120.20748410.9890.0630.2176.09799.3
3.32-3.5311.40.18648110.9890.0580.1968.11699.3
3.531-3.810.90.16348480.9910.0510.1719.67799.1
3.802-4.188.90.13346970.9910.0470.14111.1296.1
4.182-4.799.80.12347280.9910.0410.1313.55996.3
4.792-6.0312.10.11649040.9930.0350.12112.55499.2
6.034-5012.10.07350640.9980.0220.0778.71998.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LNI

4lni


Resolution: 2.801→40.573 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 2484 5.2 %
Rwork0.2003 45277 -
obs0.203 47761 96.61 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.074 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 131.24 Å2 / Biso mean: 57.13 Å2 / Biso min: 30.41 Å2
Baniso -1Baniso -2Baniso -3
1-22.7721 Å20 Å2-0 Å2
2--5.926 Å20 Å2
3----28.6982 Å2
Refinement stepCycle: final / Resolution: 2.801→40.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9663 0 0 0 9663
Num. residues----1263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099903
X-RAY DIFFRACTIONf_angle_d1.21613458
X-RAY DIFFRACTIONf_chiral_restr0.081455
X-RAY DIFFRACTIONf_plane_restr0.0051782
X-RAY DIFFRACTIONf_dihedral_angle_d15.6163546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8013-2.85520.40341090.2868203279
2.8552-2.91340.33431220.2843245895
2.9134-2.97680.32761150.2643251897
2.9768-3.0460.34511590.2548249698
3.046-3.12210.33441340.2556253598
3.1221-3.20650.33571460.2645253498
3.2065-3.30080.30611610.2434248698
3.3008-3.40730.29161560.2449254098
3.4073-3.5290.28371460.2119251999
3.529-3.67020.28041320.2072256798
3.6702-3.83720.21881360.1887253698
3.8372-4.03930.22981240.1771251296
4.0393-4.29210.24461240.1627244393
4.2921-4.62310.17651470.143254197
4.6231-5.08750.18051430.1506257098
5.0875-5.82180.26791510.2035260799
5.8218-7.32790.2661310.21522665100
7.3279-40.5730.19241480.1804271898

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