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- PDB-2bvc: Crystal structure of Mycobacterium tuberculosis glutamine synthet... -

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Basic information

Entry
Database: PDB / ID: 2bvc
TitleCrystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic
ComponentsGLUTAMINE SYNTHETASE 1
KeywordsLIGASE / TRANSITION STATE MIMIC / 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
ADENOSINE-5'-DIPHOSPHATE / L-METHIONINE-S-SULFOXIMINE PHOSPHATE / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKrajewski, W.W. / Jones, T.A. / Mowbray, S.L.
CitationJournal: 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
DepositionJun 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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)332,28342
Polymers327,5086
Non-polymers4,77536
Water11,187621
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)664,56684
Polymers655,01712
Non-polymers9,54972
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)133.261, 229.457, 203.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 4 - 478 / Label seq-ID: 12 - 486

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase

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Non-polymers , 5 types, 657 molecules

#2: Chemical
ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE


Mass: 260.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H13N2O6PS
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 6.8 / Details: 30% PEG400, 0.1M MES PH6.8, 200 MM MGCL2, pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 160432 / % possible obs: 89.6 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.4 / % possible all: 69.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTO

1hto


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.036 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 8011 5 %RANDOM
Rwork0.191 ---
obs0.193 152255 89.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---1.47 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22572 0 276 621 23469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02223466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.96631950
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63752844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51824.1971158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.776153624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.09715126
X-RAY DIFFRACTIONr_chiral_restr0.0750.23342
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218426
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1850.29769
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.215913
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.21010
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.2329
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.257
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3721.514705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.637223004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91310087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4064.58946
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: 3762 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.215
2Bloose positional0.185
3Cloose positional0.195
4Dloose positional0.175
5Eloose positional0.285
6Floose positional0.175
1Aloose thermal1.3710
2Bloose thermal1.7610
3Cloose thermal2.0210
4Dloose thermal1.1810
5Eloose thermal2.1710
6Floose thermal1.3910
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 441
Rwork0.268 7990

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