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- PDB-7cqu: GmaS/ADP/MetSox-P complex -

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Basic information

Entry
Database: PDB / ID: 7cqu
TitleGmaS/ADP/MetSox-P complex
ComponentsType III glutamate--ammonia ligase
KeywordsLIGASE / GMA synthetase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


glutamine synthetase / polyamine catabolic process / glutamine biosynthetic process / glutamine synthetase activity / nitrogen fixation / nucleotide binding / metal ion binding
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
ADENOSINE-5'-DIPHOSPHATE / L-METHIONINE-S-SULFOXIMINE PHOSPHATE / Type III glutamate--ammonia ligase
Similarity search - Component
Biological speciesRhodovulum sp. 12E13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,87318
Polymers146,5923
Non-polymers2,28115
Water23,6001310
1
A: Type III glutamate--ammonia ligase
B: Type III glutamate--ammonia ligase
C: Type III glutamate--ammonia ligase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)595,49472
Polymers586,37012
Non-polymers9,12460
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area76450 Å2
ΔGint-807 kcal/mol
Surface area157830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.598, 174.727, 190.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-931-

HOH

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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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE


Mass: 260.205 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H13N2O6PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1310 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M bicine (pH 8.5), 10% (v/v) 2-propanol, 30% (v/v) polyethylene glycol 1500

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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: May 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 114519 / % possible obs: 97.5 % / Redundancy: 4 % / Biso Wilson estimate: 20.98 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.048 / Rrim(I) all: 0.102 / Χ2: 4.035 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1830.46110400.8110.2860.5462.06994.5
2.18-2.263.10.382110740.8420.2380.4542.79995.5
2.26-2.3730.321110960.8730.2060.3833.31895.1
2.37-2.493.50.292112480.8940.1720.3414.19296.8
2.49-2.653.60.258113590.9110.1480.35.1397.1
2.65-2.853.50.183114180.9080.1080.2144.27597.6
2.85-3.1440.112115880.9830.0630.132.92398.9
3.14-3.594.50.086117350.9920.0450.0973.66399.7
3.59-4.525.30.061118280.9960.0290.0684.181100
4.52-5060.043121330.9960.0190.0485.541100

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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: 7CQL

7cql


Resolution: 2.06→36.896 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 5240 5.01 %
Rwork0.163 99290 -
obs0.165 104530 87.28 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.597 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 90.18 Å2 / Biso mean: 24.33 Å2 / Biso min: 9.42 Å2
Baniso -1Baniso -2Baniso -3
1-6.9763 Å2-0 Å2-0 Å2
2---1.1898 Å20 Å2
3----5.7865 Å2
Refinement stepCycle: final / Resolution: 2.06→36.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 135 1310 11276
Biso mean--18.83 31.43 -
Num. residues----1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710216
X-RAY DIFFRACTIONf_angle_d1.12513927
X-RAY DIFFRACTIONf_chiral_restr0.0741507
X-RAY DIFFRACTIONf_plane_restr0.0051822
X-RAY DIFFRACTIONf_dihedral_angle_d16.2973741
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0603-2.08370.2146700.224115131
2.0837-2.10820.27051620.2117289078
2.1082-2.13390.27321410.2057296479
2.1339-2.16090.25331550.1971304280
2.1609-2.18930.22681720.1949303881
2.1893-2.21930.26721460.1956300680
2.2193-2.2510.2541630.1933305781
2.251-2.28460.23481770.1925303481
2.2846-2.32030.23041730.1917310683
2.3203-2.35840.23821670.1837315084
2.3584-2.3990.23421490.194319184
2.399-2.44260.24941580.1826324886
2.4426-2.48960.22171660.1896321885
2.4896-2.54040.23941710.1804324587
2.5404-2.59560.23211900.1715330488
2.5956-2.6560.23851600.1707338389
2.656-2.72240.21381890.1794335189
2.7224-2.7960.19151840.1837337790
2.796-2.87820.22951920.1688343991
2.8782-2.97110.22721980.1774353194
2.9711-3.07720.20221700.1693360394
3.0772-3.20040.20891780.1755363196
3.2004-3.34590.20572020.1761366497
3.3459-3.52220.21541700.1666371997
3.5222-3.74270.20841950.1514376698
3.7427-4.03130.17511890.131376098
4.0313-4.43640.13611960.1142381099
4.4364-5.0770.13892230.1131381199
5.077-6.3910.17571970.14893873100
6.391-36.8960.1722370.1604392898

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