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- PDB-3ng0: Crystal Structure of Glutamine Synthetase from Synechocystis sp. ... -

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Basic information

Entry
Database: PDB / ID: 3ng0
TitleCrystal Structure of Glutamine Synthetase from Synechocystis sp. PCC 6803
ComponentsGlutamine synthetase
KeywordsLIGASE / Glutamine synthetase type I / GSI / Nitrogen Metabolism / Synechocystis
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / 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 / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / 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 / : / Glutamine synthetase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSaelices, L. / Cascio, D. / Florencio, F.J. / Muro-Pastor, M.I.
CitationJournal: To be Published
Title: Crystal Structure of Glutamine Synthetase from Synechocystis sp. PCC 6803
Authors: Saelices, L. / Cascio, D. / Florencio, F.J. / Muro-Pastor, M.I.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7255
Polymers53,0541
Non-polymers6714
Water43224
1
A: Glutamine synthetase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)644,69560
Polymers636,64312
Non-polymers8,05248
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation9_556-x,-x+y,-z+11
crystal symmetry operation10_556-y,-x,-z+11
crystal symmetry operation11_556-x+y,y,-z+11
crystal symmetry operation12_556x,x-y,-z+11
Buried area99130 Å2
ΔGint-761 kcal/mol
Surface area173520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.016, 132.016, 202.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Glutamine synthetase / / Glutamate--ammonia ligase


Mass: 53053.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: glnA, slr1756 / Plasmid: pBS-SK+ / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P77961, glutamine synthetase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS CRYSTAL CONTAINS 2 MOLECULES PER ASYMMETRIC UNIT. P622 CRYSTAL SYMMETRY GENERATES TWO ...THIS CRYSTAL CONTAINS 2 MOLECULES PER ASYMMETRIC UNIT. P622 CRYSTAL SYMMETRY GENERATES TWO DODECAMERS (BIOLOGICAL UNITS) IN THE UNIT CELL, ONE DODECAMER FROM EACH MONOMER. UNIT CELL TRANSLATIONS ALONG A AND B GENERATE LAYERS IN THE CRYSTAL COMPOSED OF DODECAMER 1 WHICH ARE INTERLEAVED BY SIMILAR LAYERS COMPOSED OF DODECAMER 2. TRANSLOCATION LATTICE DEFECTS (TLD) COMPLICATE THE INTERPRETATION OF THE ELECTRON DENSITY FOR DODECAMER 2. THIS DODECAMER IS DISTRIBUTED RANDOMLY OVER 6 DIFFERENT POSITIONS (DIFFERING IN X,Y COORDINATES) WITHIN THE LAYER. TO FACILITATE INTERPRETATION OF THE ELECTRON DENSITY MAP, THE CONTRIBUTION FROM DODECAMER 2 HAS BEEN REMOVED FROM THE STRUCTURE FACTORS BY APPLYING A LATTICE TRANSLOCATION CORRECTION. ACCORDINGLY, THE COORDINATES FOR THE SECOND MOLECULE ARE NOT INCLUDED IN THIS PDB ENTRY.

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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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium acetate,0.1M calcium acetate, 10% PEG 4000, pH 4.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 25802 / % possible obs: 98 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.56 Å2 / Rmerge(I) obs: 0.213 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.96.80.424199.2
2.9-3.026.80.37199.5
3.02-3.156.80.302199.3
3.15-3.326.80.274199.1
3.32-3.536.90.233198.7
3.53-3.86.70.21198.7
3.8-4.186.80.196198.4
4.18-4.796.50.178197.5
4.79-6.036.70.176197.2
6.03-1006.30.157193.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å99.51 Å
Translation2.8 Å99.51 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→32.92 Å / Cor.coef. Fo:Fc: 0.8182 / Cor.coef. Fo:Fc free: 0.7756 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3129 1298 5.04 %RANDOM
Rwork0.2853 ---
obs0.2867 25779 --
Displacement parametersBiso mean: 28.98 Å2
Baniso -1Baniso -2Baniso -3
1-6.6465 Å20 Å20 Å2
2--6.6465 Å20 Å2
3----13.293 Å2
Refine analyzeLuzzati coordinate error obs: 0.546 Å
Refinement stepCycle: LAST / Resolution: 2.8→32.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 34 24 3732
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093811HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.165180HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1299SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes546HARMONIC5
X-RAY DIFFRACTIONt_it3778HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion21.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4855
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact44734
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3443 124 4.4 %
Rwork0.3031 2693 -
all0.3048 2817 -

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