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- PDB-2d3b: Crystal Structure of the Maize Glutamine Synthetase complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2d3b
TitleCrystal Structure of the Maize Glutamine Synthetase complexed with AMPPNP and Methionine sulfoximine
Componentsglutamine synthetase
KeywordsLIGASE / GLUTAMINE SYNTHETASE MAIZE
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. ...Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / 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 / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / (2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID / Glutamine synthetase root isozyme 3
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3.5 Å
AuthorsUnno, H. / Uchida, T. / Sugawara, H. / Kurisu, G. / Sugiyama, T. / Yamaya, T. / Sakakibara, H. / Hase, T. / Kusunoki, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Atomic Structure of Plant Glutamine Synthetase: A KEY ENZYME FOR PLANT PRODUCTIVITY
Authors: Unno, H. / Uchida, T. / Sugawara, H. / Kurisu, G. / Sugiyama, T. / Yamaya, T. / Sakakibara, H. / Hase, T. / Kusunoki, M.
History
DepositionSep 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
G: glutamine synthetase
H: glutamine synthetase
I: glutamine synthetase
J: glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,15360
Polymers392,64010
Non-polymers8,51250
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59930 Å2
ΔGint-332 kcal/mol
Surface area114630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.881, 190.943, 117.904
Angle α, β, γ (deg.)90.00, 101.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 3 - 355 / Label seq-ID: 3 - 355

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ

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Components

#1: Protein
glutamine synthetase /


Mass: 39264.039 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: gs1a / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / References: UniProt: P38561, glutamine synthetase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MSL / (2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID / METHIONINE SULFOXIMINE / Methionine sulfoximine


Type: L-peptide linking / Mass: 180.225 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C5H12N2O3S / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 9% PEG8000, 5% MPD, 100MM Tris-HCl, 10MM MnCl2, 1MM AMPPNP, 1MM L-Methionine sulfoximine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jul 14, 2004
RadiationMonochromator: Osmic conforcal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 41598 / % possible obs: 75.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.81
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 2.32 / % possible all: 78.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 3.5→33.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 24.94 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.655 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20905 2227 5.1 %RANDOM
Rwork0.16584 ---
obs0.16804 41315 83.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.5→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27450 0 450 377 28277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02228630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.96839020
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5553520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19823.9841280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.605154460
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.04215180
X-RAY DIFFRACTIONr_chiral_restr0.1010.24040
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.212993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.219192
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4330.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6711.517776
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.143228210
X-RAY DIFFRACTIONr_scbond_it1.46312736
X-RAY DIFFRACTIONr_scangle_it2.3484.510810
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2746 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.050.05
3Ctight positional0.050.05
4Dtight positional0.050.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.050.05
8Htight positional0.050.05
9Itight positional0.050.05
10Jtight positional0.050.05
1Atight thermal0.070.5
2Btight thermal0.090.5
3Ctight thermal0.080.5
4Dtight thermal0.090.5
5Etight thermal0.080.5
6Ftight thermal0.080.5
7Gtight thermal0.080.5
8Htight thermal0.110.5
9Itight thermal0.070.5
10Jtight thermal0.090.5
LS refinement shellResolution: 3.499→3.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 169 -
Rwork0.207 3125 -
obs--85.78 %

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