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- PDB-2whi: Crystal structure of Mycobacterium Tuberculosis Glutamine Synthet... -

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Basic information

Entry
Database: PDB / ID: 2whi
TitleCrystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with a purine analogue inhibitor and L-methionine-S- sulfoximine phosphate.
ComponentsGLUTAMINE SYNTHETASE 1
KeywordsLIGASE / NUCLEOTIDE-BINDING / TRANSITION STATE MIMIC / TAUT STATE / ATP-BINDING / PURINE ANALOGUE / GLNA1 / MT2278 / RV2220 / CYTOPLASM / SYNTHETASE
Function / homology
Function and homology information


nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization ...nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / 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 ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / 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
Chem-1AZ / L-METHIONINE-S-SULFOXIMINE PHOSPHATE / PHOSPHATE ION / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNilsson, M.T. / Krajewski, W.W. / Jones, T.A. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structural Basis for the Inhibition of Mycobacterium Tuberculosis Glutamine Synthetase by Novel ATP-Competitive Inhibitors.
Authors: Nilsson, M.T. / Krajewski, W.W. / Yellagunda, S. / Prabhumurthy, S. / Chamarahally, G.N. / Siddamadappa, C. / Srinivasa, B.R. / Yahiaoui, S. / Larhed, M. / Karlen, A. / Jones, T.A. / Mowbray, S.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of Mycobacterium Tuberculosis Glutamine Synthetase in Complex with a Transition-State Mimic Provides Functional Insights.
Authors: Krajewski, W.W. / Jones, T.A. / Mowbray, S.L.
History
DepositionMay 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,26554
Polymers327,5086
Non-polymers6,75748
Water29,7071649
1
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules

A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)668,530108
Polymers655,01712
Non-polymers13,51396
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area107920 Å2
ΔGint-1111.41 kcal/mol
Surface area168720 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33990 Å2
ΔGint-444.51 kcal/mol
Surface area104330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.210, 228.760, 202.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2058-

HOH

21F-2096-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 402
2111B3 - 402
3111C3 - 402
4111D3 - 402
5111E3 - 402
6111F3 - 402
1211A417 - 882
2211B417 - 882
3211C417 - 882
4211D417 - 882
5211E417 - 882
6211F417 - 882

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
GLUTAMINE SYNTHETASE 1 / / GLUTAMATE--AMMONIA LIGASE 1


Mass: 54584.730 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PTRC99C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745
References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase

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Non-polymers , 7 types, 1697 molecules

#2: Chemical
ChemComp-1AZ / 1-(3,4-dichlorobenzyl)-3,7-dimethyl-8-morpholin-4-yl-3,7-dihydro-1H-purine-2,6-dione


Mass: 424.281 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H19Cl2N5O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE


Mass: 260.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H13N2O6PS
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1649 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE ...PROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE PURIFICATION TAG.

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Description: PROTEIN ONLY COORDINATES FROM THE ISOMORPHOUS CRYSTAL FORM FOUND IN PDB ENTRY 2BVC WERE USED AS THE STARTING POINT FOR REFINEMENT.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M MES, PH 6.8, 0.2 M MAGNESIUM CHLORIDE, 40% (V/V) PEG400) AND PROTEIN SOLUTION (30 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M ...Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M MES, PH 6.8, 0.2 M MAGNESIUM CHLORIDE, 40% (V/V) PEG400) AND PROTEIN SOLUTION (30 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M MAGNESIUM CHLORIDE, 4%(V/V) DMSO, 0.001 M INHIBITOR, 0.004 M MSOP), HANGING-DROP, VAPOR DIFFUSION, TEMPERATURE 294K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→39.8 Å / Num. obs: 151747 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.4 / % possible all: 86.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVC

2bvc


Resolution: 2.2→39.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.307 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 403-416 ARE EXCLUDED FROM THE NCS DUE TO DIFFERENCES AS A RESULT OF CRYSTAL CONTACTS. E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 403-416 ARE EXCLUDED FROM THE NCS DUE TO DIFFERENCES AS A RESULT OF CRYSTAL CONTACTS. E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE DEFICIENT ( GLNE-) LONG CONTINUOUS DENSITY WAS MODELED AS PEG BASED ON THE HIGH PEG400 CONTENT IN THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23116 7666 5 %RANDOM
Rwork0.21085 ---
obs0.21186 145335 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---1.81 Å20 Å2
3---1.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22626 0 408 1649 24683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02223646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9732148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65852850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89724.2271164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.746153636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7815126
X-RAY DIFFRACTIONr_chiral_restr0.0750.23324
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218552
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.210224
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.215969
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.21488
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2392
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.2129
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3621.514670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.636223052
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.825310428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3884.59096
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4004 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
4Dtight positional0.030.05
5Etight positional0.030.05
6Ftight positional0.030.05
1Atight thermal0.060.5
2Btight thermal0.060.5
3Ctight thermal0.070.5
4Dtight thermal0.060.5
5Etight thermal0.060.5
6Ftight thermal0.060.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 512 -
Rwork0.329 9320 -
obs--85.94 %

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