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- PDB-7cqq: GmaS in complex with AMPPNP and MetSox -

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Basic information

Entry
Database: PDB / ID: 7cqq
TitleGmaS in complex with AMPPNP and MetSox
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / (2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID / Type III glutamate--ammonia ligase
Similarity search - Component
Biological speciesRhodovulum sp. 12E13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.295 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)148,87018
Polymers146,5923
Non-polymers2,27815
Water15,133840
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)595,48272
Polymers586,37012
Non-polymers9,11260
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area71170 Å2
ΔGint-655 kcal/mol
Surface area156640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.553, 174.476, 190.125
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
#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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MSL / (2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID / METHIONINE SULFOXIMINE


Type: L-peptide linking / Mass: 180.225 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12N2O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 3.27 Å3/Da / Density % sol: 62.37 %
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: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.295→50 Å / Num. obs: 85608 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.79 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 0.697 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3460.44942140.9140.1990.4920.459100
2.34-2.386.50.42142440.9370.1780.4580.46100
2.38-2.436.50.37642480.9560.1580.4080.469100
2.43-2.486.50.33842510.9580.1430.3670.48100
2.48-2.536.40.31842450.9610.1350.3460.484100
2.53-2.596.40.27342300.9690.1160.2970.496100
2.59-2.666.30.24542340.9690.1050.2670.505100
2.66-2.736.20.22642400.9760.0990.2470.53100
2.73-2.815.90.19742760.9780.0890.2170.543100
2.81-2.96.20.16542590.9850.0720.180.577100
2.9-36.60.1542610.9880.0630.1630.621100
3-3.126.60.12742630.9910.0530.1370.673100
3.12-3.266.60.10642630.9920.0450.1150.738100
3.26-3.446.50.08842920.9950.0380.0960.844100
3.44-3.656.20.07742820.9950.0340.0840.969100
3.65-3.936.60.06542910.9970.0270.071.056100
3.93-4.336.90.05843140.9970.0230.0621.213100
4.33-4.956.70.05143080.9980.0210.0561.148100
4.95-6.246.30.04843660.9980.0210.0530.881100
6.24-506.40.03745270.9990.0160.040.6699.9

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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: 2.295→31.826 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 4099 5.04 %
Rwork0.1572 77254 -
obs0.1591 81353 94.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.562 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 106.59 Å2 / Biso mean: 37.17 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1-11.3247 Å2-0 Å2-0 Å2
2---0.7238 Å20 Å2
3----10.6009 Å2
Refinement stepCycle: final / Resolution: 2.295→31.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 135 840 10806
Biso mean--34.32 41.1 -
Num. residues----1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710212
X-RAY DIFFRACTIONf_angle_d1.12113920
X-RAY DIFFRACTIONf_chiral_restr0.0681509
X-RAY DIFFRACTIONf_plane_restr0.0051821
X-RAY DIFFRACTIONf_dihedral_angle_d17.6813738
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2952-2.32220.29641280.2053231383
2.3222-2.35050.25181440.1837244288
2.3505-2.38030.25311260.1868245789
2.3803-2.41160.25411260.1741249989
2.4116-2.44460.24221330.1709251190
2.4446-2.47950.20231370.171251190
2.4795-2.51650.21321150.175256992
2.5165-2.55580.22671220.173257692
2.5558-2.59770.23441530.1718255193
2.5977-2.64250.22551360.1732258693
2.6425-2.69050.23611450.1797261494
2.6905-2.74220.23641540.182257793
2.7422-2.79820.26891350.1854266095
2.7982-2.8590.23171320.1771263195
2.859-2.92550.22891440.1804267395
2.9255-2.99860.21411280.1881269896
2.9986-3.07960.23211550.1774271797
3.0796-3.17010.2421580.1887269897
3.1701-3.27230.2281320.1876275297
3.2723-3.38920.24191360.1791274998
3.3892-3.52470.19251630.1682277298
3.5247-3.68490.19251460.1568275199
3.6849-3.87880.17571520.1456279099
3.8788-4.12140.16731390.1257282599
4.1214-4.43880.15361500.11372826100
4.4388-4.88410.1211490.11242843100
4.8841-5.58750.16251640.1332832100
5.5875-7.02720.18521400.15592895100
7.0272-31.8260.14781570.1478293698

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