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- PDB-1htq: Multicopy crystallographic structure of a relaxed glutamine synth... -

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Basic information

Entry
Database: PDB / ID: 1htq
TitleMulticopy crystallographic structure of a relaxed glutamine synthetase from Mycobacterium tuberculosis
Componentsglutamine synthetase
KeywordsLIGASE / glutamine synthetase / Mycobacterium tuberculosis / multicopy refinement / 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 / Multicopy Refinement / Resolution: 2.4 Å
AuthorsGill, H.S. / Pfluegl, G.M. / 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 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 area99070 Å2
ΔGint-462 kcal/mol
Surface area182800 Å2
MethodPISA
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 area99100 Å2
ΔGint-463 kcal/mol
Surface area182790 Å2
MethodPISA
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
Number of models10
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: 2.86 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering 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: Multicopy Refinement
Starting model: 1HTO

1hto


Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: THE AVERAGED-SUBUNIT (MONOMERIC) MODEL OF THE PDB ENTRY 1HTO WAS FURTHER REFINED HERE BY DUPLICATING 10 COPIES OF THE MONOMERIC MODEL WITH 24-FOLD STRICT NCS-AVERAGING CONSTRAINTS IMPOSED ON ...Details: THE AVERAGED-SUBUNIT (MONOMERIC) MODEL OF THE PDB ENTRY 1HTO WAS FURTHER REFINED HERE BY DUPLICATING 10 COPIES OF THE MONOMERIC MODEL WITH 24-FOLD STRICT NCS-AVERAGING CONSTRAINTS IMPOSED ON EACH MODEL. THE ENTIRE ENSEMBLE WAS THEN SIMULTANEOUSLY REFINED AGAINST THE DATA BY SIMULATED ANNEALING PROTOCOLS WITH A FIXED OVERALL B-FACTOR AND 0.1 PARTIAL OCCUPANCIES ASSIGNED TO EACH OF THE TEN MODELS, USING PROGRAM XPLOR 3.843. CHEMICALLY EACH COPY OR CHAIN DOES NOT SEE ONE ANOTHER DURING REFINEMENT, BUT EACH ADDS TOGETHER TO CALCULATE THE TOTAL STRUCTURE FACTOR. POSITIONAL AND B-FACTOR REFINEMENT WERE OPTIONALLY EMPLOYEED TO EACH OF THE 10 MODELS THEREAFTER. LIGANDS AND WATERS WERE ALSO OPTIONALLY FIXED DURING THE REFINEMENT. THIS REPRESENTATIVE ENTRY EMPLOYEED POSITIONAL AND B-FACTOR REFINEMENT AFTER SIMULATED ANNEALING WITH ONLY THE LIGANDS FIXED DURING REFINEMENT. ALL RESULTS INDICATED A DROP IN BOTH THE R-FACTOR AND R-FREE FROM THE 1HT0 ENTRY, AND APPEAR STRUCTURALLY SIMILAR. THE FULL ASYMMETRIC UNIT WAS SUBSEQUENTLY GENERATED FOR EACH OF THE 10 COPIES BY APPLYING THE 24-FOLD NCS-SYMMETRY AND IN TOTAL CONTAINS APPROXIMATELY 1 MILLION ATOMS. THE MULTICOPY MODEL HIGHLIGHTS MOVEMENTS OF CATALYTIC AND REGULATORY LOOPS IN GLUTAMINE SYNTHESIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 16756 -RANDOM
Rwork0.204 ---
all0.205 566314 --
obs0.205 566314 99.6 %-
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_d0.009
X-RAY DIFFRACTIONx_angle_d1.5

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