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- PDB-7cqn: GmaS in complex with AMPPCP -

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Basic information

Entry
Database: PDB / ID: 7cqn
TitleGmaS in complex with AMPPCP
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Type III glutamate--ammonia ligase
Similarity search - Component
Biological speciesRhodovulum sp. 12E13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.962 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)148,1086
Polymers146,5923
Non-polymers1,5163
Water29,1481618
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)592,43224
Polymers586,37012
Non-polymers6,06212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area69030 Å2
ΔGint-244 kcal/mol
Surface area157490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.917, 176.701, 191.833
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
11A-783-

HOH

21A-842-

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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1618 / 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: 3.21 Å3/Da / Density % sol: 61.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 0.2 M ammonium acetate and 25% (v/v) isopropanol

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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 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. obs: 131664 / % possible obs: 98.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Rrim(I) all: 0.09 / Χ2: 1.328 / Net I/σ(I): 8 / Num. measured all: 600254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.96-1.992.90.40558640.8450.2570.4830.47387.7
1.99-2.033.20.30862550.8940.1890.3640.47394.4
2.03-2.073.30.3963510.1570.2390.4610.89795.8
2.07-2.113.50.26964440.7850.1580.3140.56896.4
2.11-2.163.50.21664700.950.1270.2530.50197.6
2.16-2.213.70.22865060.960.1310.2650.55797.5
2.21-2.263.70.31965400.8190.1780.3682.9798.2
2.26-2.323.80.26965390.9570.1540.3120.83398.1
2.32-2.394.20.13966050.9820.0740.1580.54699.3
2.39-2.474.50.12766320.9860.0660.1440.56799.6
2.47-2.564.60.13666580.9870.070.1540.6699.7
2.56-2.664.60.10266770.990.0530.1160.67199.6
2.66-2.784.50.166700.4040.0530.1130.74799.4
2.78-2.934.90.0866470.9940.0390.0890.74999.6
2.93-3.115.50.06867030.9960.0320.0750.81299.9
3.11-3.355.80.05967450.9970.0270.0650.948100
3.35-3.695.70.06767370.9960.0310.0741.476100
3.69-4.226.50.0567610.9980.0210.0551.281100
4.22-5.326.20.03768250.9990.0160.0411.197100
5.32-506.10.03970350.9950.0170.0436.07499.9

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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: 1.962→37.493 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 6215 5.03 %
Rwork0.1673 117429 -
obs0.1689 123644 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.312 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 98.28 Å2 / Biso mean: 18.93 Å2 / Biso min: 3.88 Å2
Baniso -1Baniso -2Baniso -3
1-5.1176 Å2-0 Å2-0 Å2
2---1.7566 Å20 Å2
3----3.361 Å2
Refinement stepCycle: final / Resolution: 1.962→37.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9831 0 186 1618 11635
Biso mean--17.93 29.17 -
Num. residues----1287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710300
X-RAY DIFFRACTIONf_angle_d1.06314063
X-RAY DIFFRACTIONf_chiral_restr0.0711520
X-RAY DIFFRACTIONf_plane_restr0.0051827
X-RAY DIFFRACTIONf_dihedral_angle_d17.5273831
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.962-1.98420.23051760.2069283968
1.9842-2.00750.21911680.1883347282
2.0075-2.0320.23791650.1825364886
2.032-2.05770.23692110.1779366687
2.0577-2.08480.21562270.1788371188
2.0848-2.11330.21092220.1754370489
2.1133-2.14350.2231920.1727379290
2.1435-2.17550.20471890.1708386291
2.1755-2.20950.22221790.2006339981
2.2095-2.24570.35361530.2844314074
2.2457-2.28440.37672220.3297346983
2.2844-2.3260.2321770.1937346982
2.326-2.37070.23311930.1606401395
2.3707-2.41910.19561970.1677403096
2.4191-2.47170.22922480.1672401496
2.4717-2.52920.20762180.1625412097
2.5292-2.59240.2062090.1605408597
2.5924-2.66250.20462180.1608413497
2.6625-2.74080.19072130.167410497
2.7408-2.82920.20472000.1667415298
2.8292-2.93030.20192200.1583416998
2.9303-3.04760.192120.1576420199
3.0476-3.18620.18352230.1494423099
3.1862-3.35410.16322020.1513425399
3.3541-3.56410.18392580.1529418599
3.5641-3.8390.16432180.1559422598
3.839-4.22490.15632330.1312423999
4.2249-4.83520.12622100.12354323100
4.8352-6.08760.18742430.1524321100
6.0876-37.4930.17522190.1721446098

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