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- PDB-2a9v: Crystal structure of a putative gmp synthase subunit a protein (t... -

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Basic information

Entry
Database: PDB / ID: 2a9v
TitleCrystal structure of a putative gmp synthase subunit a protein (ta0944m) from thermoplasma acidophilum at 2.45 A resolution
ComponentsGMP synthase
KeywordsLIGASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
THIOCYANATE ION / GMP synthase [glutamine-hydrolyzing] subunit A
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular replacement / MAD / Resolution: 2.24 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_394403.1) from THERMOPLASMA ACIDOPHILUM at 2.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GMP synthase
B: GMP synthase
C: GMP synthase
D: GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,37317
Polymers96,4024
Non-polymers97113
Water3,801211
1
A: GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2513
Polymers24,1011
Non-polymers1502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2864
Polymers24,1011
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4015
Polymers24,1011
Non-polymers3004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4355
Polymers24,1011
Non-polymers3344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)275.661, 39.045, 68.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
GMP synthase / / Glutamine amidotransferase


Mass: 24100.541 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: guaAA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HJM3, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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 Å3/Da / Density % sol: 37.99 %
Description: THE SELENIUM SUBSTRUCTURE WAS SOLVED INITIALLY FROM AN ANOMALOUS DIFFERENCE FOURIER BASED ON A PREVIOUS MOLECULAR REPLACEMENT SOLUTION. THE PHASES WERE THEN REFINED IN SHARP. THE BEST ...Description: THE SELENIUM SUBSTRUCTURE WAS SOLVED INITIALLY FROM AN ANOMALOUS DIFFERENCE FOURIER BASED ON A PREVIOUS MOLECULAR REPLACEMENT SOLUTION. THE PHASES WERE THEN REFINED IN SHARP. THE BEST WARPNTRACE RESULT WAS GENERATED FROM THE MOLECULAR REPLACEMENT MODEL, USING THE MAD PHASES AS PHASE RESTRAINTS FOR REFMAC WITH THE MLHL TARGET.THE SUBSTRUCTURE CAN BE DETERMINED DE NOVO USING SHELXD AND AUTOSHARP. HOWEVER, THE TRACING RESULT IS NOT AS GOOD AS THE TRACE OBTAINED WITH BOTH MAD AND MOLECULAR REPLACEMENT CONTRIBUTIONS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 22.00% PEG 3350, 0.20M NP_Sodium Thiocyanate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00, 0.97971, 0.97947
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979711
30.979471
ReflectionResolution: 2.24→66.27 Å / Num. obs: 29096 / % possible obs: 78.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.24-2.330.71.50.1634.88470.163
2.3-2.36371.50.2043.89460.204
2.36-2.4349.520.1764.212700.176
2.43-2.557.720.1435.114100.143
2.5-2.5966.52.40.123616120.123
2.59-2.6874.32.50.1086.717150.108
2.68-2.7883.430.0997.118950.099
2.78-2.8995.33.40.0858.320330.085
2.89-3.021003.80.0798.621100.079
3.02-3.171003.70.0699.319550.069
3.17-3.341003.70.06210.318880.062
3.34-3.541003.80.05711.118300.057
3.54-3.791003.60.05111.716760.051
3.79-4.0999.83.70.04612.815860.046
4.09-4.4899.63.70.0451214620.045
4.48-5.0199.83.60.0431213450.043
5.01-5.781003.50.04910.512040.049
5.78-7.0899.43.40.04611.410180.046
7.08-10.02993.20.0411.18170.04
10.02-66.2697.43.20.0429.14770.042

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
SHARPphasing
ARP/wARPmodel building
SHELXDphasing
RefinementMethod to determine structure: MAD, Molecular replacement
Starting model: 1qdl

1qdl


Resolution: 2.24→66.27 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.757 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.952 / ESU R Free: 0.295
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NOMINAL RESOLUTION IS 2.45 A WITH 3445 OBSERVED REFLECTIONS BETWEEN 2.45-2.24 (40.4% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1439 5 %RANDOM
Rwork0.176 ---
all0.179 ---
obs-27616 79.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.529 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.83 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.24→66.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6283 0 58 211 6552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216498
X-RAY DIFFRACTIONr_bond_other_d0.0050.024314
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9378800
X-RAY DIFFRACTIONr_angle_other_deg0.983310518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4424.599324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.829151046
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2371529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027290
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021315
X-RAY DIFFRACTIONr_nbd_refined0.2020.21287
X-RAY DIFFRACTIONr_nbd_other0.1950.24419
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23128
X-RAY DIFFRACTIONr_nbtor_other0.0880.23371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.273
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.220
X-RAY DIFFRACTIONr_mcbond_it0.4941.53952
X-RAY DIFFRACTIONr_mcbond_other0.1531.51630
X-RAY DIFFRACTIONr_mcangle_it1.04726372
X-RAY DIFFRACTIONr_scbond_it2.09232546
X-RAY DIFFRACTIONr_scangle_it3.2934.52426
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 46 -
Rwork0.207 800 -
obs--31.11 %

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