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- PDB-1hto: CRYSTALLOGRAPHIC STRUCTURE OF A RELAXED GLUTAMINE SYNTHETASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1hto
TitleCRYSTALLOGRAPHIC STRUCTURE OF A RELAXED GLUTAMINE SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsGLUTAMINE SYNTHETASE
KeywordsLIGASE / glutamine synthetase / Mycobacterium tuberculosis / Citrate / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding ...nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / 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 MONOPHOSPHATE / CITRIC ACID / : / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGill, H.S. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochemistry / Year: 2002
Title: Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation.
Authors: Gill, H.S. / Pfluegl, G.M. / Eisenberg, D.
History
DepositionJan 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: 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_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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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

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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
K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
M: GLUTAMINE SYNTHETASE
N: GLUTAMINE SYNTHETASE
O: GLUTAMINE SYNTHETASE
P: GLUTAMINE SYNTHETASE
Q: GLUTAMINE SYNTHETASE
R: GLUTAMINE SYNTHETASE
S: GLUTAMINE SYNTHETASE
T: GLUTAMINE SYNTHETASE
U: GLUTAMINE SYNTHETASE
V: GLUTAMINE SYNTHETASE
W: GLUTAMINE SYNTHETASE
X: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,298,18096
Polymers1,283,91724
Non-polymers14,26372
Water113,7116312
1
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
K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)649,09048
Polymers641,95812
Non-polymers7,13136
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area101580 Å2
ΔGint-498 kcal/mol
Surface area180380 Å2
MethodPISA, PQS
2
M: GLUTAMINE SYNTHETASE
N: GLUTAMINE SYNTHETASE
O: GLUTAMINE SYNTHETASE
P: GLUTAMINE SYNTHETASE
Q: GLUTAMINE SYNTHETASE
R: GLUTAMINE SYNTHETASE
S: GLUTAMINE SYNTHETASE
T: GLUTAMINE SYNTHETASE
U: GLUTAMINE SYNTHETASE
V: GLUTAMINE SYNTHETASE
W: GLUTAMINE SYNTHETASE
X: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)649,09048
Polymers641,95812
Non-polymers7,13136
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area101600 Å2
ΔGint-499 kcal/mol
Surface area180340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)207.720, 257.690, 274.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological complex is a dodecamer.

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Components

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


Mass: 53496.531 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: PTRCHISB / Production host: Escherichia coli (E. coli) / Strain (production host): YMC21E
References: UniProt: Q10377, UniProt: P9WN39*PLUS, glutamine synthetase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical...
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6312 / 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: 2.89 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000, sodium citrate, sodium chloride, manganese chloride, imidazole buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 1997
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 566370 / Num. obs: 566370 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 4.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Num. unique all: 80442 / % possible all: 98.8

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F52

1f52


Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE CRYSTAL PACKING WAS SOLVED USING MOLECULAR REPLACEMENT TECHNIQUES USING A DODECAMER MODEL FROM SALMONELLA TYPHIMURIUM GS AS A PROBE. THE MODEL WAS SUBSEQUENTLY REDUCED TO ONE SUBUNIT ...Details: THE CRYSTAL PACKING WAS SOLVED USING MOLECULAR REPLACEMENT TECHNIQUES USING A DODECAMER MODEL FROM SALMONELLA TYPHIMURIUM GS AS A PROBE. THE MODEL WAS SUBSEQUENTLY REDUCED TO ONE SUBUNIT WITH 24-FOLD NCS-SYMMETRICAL CONSTRAINTS IMPOSED. THE SUBUNIT WAS REFINED WITH STRICT 24-FOLD NCS-AVERAGING CONSTRAINTS AND THEN USED TO REGENERATE THE ENTIRE ASYMMETRIC UNIT. AS JUSTIFIED BY LOWER R-VALUES, THE FOLLOWING RESIDUES WERE COMPLETELY RELEASED AT THE END OF THE REFINEMENT IN ORDER ACCOMMODATE CRYSTAL CONTACTS: RESIDUES 385,98,602,11,7,40,3,292.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 16756 -RANDOM
Rwork0.227 ---
all0.228 566314 --
obs0.228 566314 99.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.32 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms90672 0 888 6312 97872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_improper_angle_d1.16
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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