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- PDB-2d7j: Crystal Structure Analysis of Glutamine Amidotransferase from Pyr... -

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Basic information

Entry
Database: PDB / ID: 2d7j
TitleCrystal Structure Analysis of Glutamine Amidotransferase from Pyrococcus horikoshii OT3
ComponentsGMP synthase [glutamine-hydrolyzing] subunit A
KeywordsLIGASE / alpha-beta-alpha
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / glutamine metabolic process / ATP binding
Similarity search - Function
GMP synthase (glutamine-hydrolyzing) subunit A / GMP synthase, glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 Å
AuthorsMaruoka, S. / Lee, W.C. / Kamo, M. / Kudo, N. / Nagata, K. / Tanokura, M.
CitationJournal: PROC.JPN.ACAD.,SER.B / Year: 2005
Title: Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3
Authors: Maruoka, S. / Lee, W.C. / Kamo, M. / Kudo, N. / Nagata, K. / Tanokura, M.
History
DepositionNov 21, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP synthase [glutamine-hydrolyzing] subunit A


Theoretical massNumber of molelcules
Total (without water)23,7181
Polymers23,7181
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.941, 64.941, 116.408
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

DetailsThis protein works as a monomer.

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Components

#1: Protein GMP synthase [glutamine-hydrolyzing] subunit A / Class I Glutamine Amidotransferase / Glutamine amidotransferase


Mass: 23718.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: O59071, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2M sodium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.974 Å
DetectorDate: Jun 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 23560
Reflection shellResolution: 1.89→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→38.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.174 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21334 1168 5 %RANDOM
Rwork0.1844 ---
all0.18584 ---
obs0.18584 22241 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.268 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.89→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 53 1550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0211531
X-RAY DIFFRACTIONr_bond_other_d0.0020.021416
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.972064
X-RAY DIFFRACTIONr_angle_other_deg1.70333320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8475187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1330.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021669
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02288
X-RAY DIFFRACTIONr_nbd_refined0.230.2273
X-RAY DIFFRACTIONr_nbd_other0.2510.21522
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0990.2900
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.441.5933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36321511
X-RAY DIFFRACTIONr_scbond_it3.8893598
X-RAY DIFFRACTIONr_scangle_it6.1624.5553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.225 91
Rwork0.177 1617
Refinement TLS params.Method: refined / Origin x: 3.5823 Å / Origin y: 26.5292 Å / Origin z: 10.4578 Å
111213212223313233
T0.0049 Å20.0231 Å2-0.0084 Å2-0.1188 Å2-0.0178 Å2--0.0567 Å2
L3.8157 °2-0.4618 °2-0.652 °2-1.7366 °20.7683 °2--2.6319 °2
S0.0033 Å °0.0265 Å °0.1468 Å °-0.1079 Å °-0.0095 Å °0.0201 Å °-0.0283 Å °0.029 Å °0.0061 Å °

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