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- PDB-3a4i: Crystal structure of GMP synthetase PH1347 from Pyrococcus horiko... -

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Basic information

Entry
Database: PDB / ID: 3a4i
TitleCrystal structure of GMP synthetase PH1347 from Pyrococcus horikoshii OT3
ComponentsGMP synthase [glutamine-hydrolyzing] subunit B
KeywordsLIGASE / ATP pyrophosphatase / glutamine amidotransferase / GMP synthetase / purine nucleotide biosynthesis / ATP-binding / GMP biosynthesis / Nucleotide-binding / Purine biosynthesis
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolysing) / ATP binding / cytosol
Similarity search - Function
GMP synthase subunit B / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / GMP Synthetase; Chain A, domain 3 / HUPs ...GMP synthase subunit B / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / GMP Synthetase; Chain A, domain 3 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing] subunit B
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMaruoka, S. / Horita, S. / Lee, W.C. / Nagata, K. / Tanokura, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of the ATPPase subunit and its substrate-dependent association with the GATase Subunit: a novel regulatory mechanism for a two-subunit-type GMP synthetase from Pyrococcus horikoshii OT3.
Authors: Maruoka, S. / Horita, S. / Lee, W.C. / Nagata, K. / Tanokura, M.
History
DepositionJul 7, 2009Deposition site: PDBJ / Processing site: PDBJ
SupersessionJul 21, 2009ID: 2Z0C
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,2202
Polymers69,2202
Non-polymers00
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-16 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.903, 82.212, 111.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GMP synthase [glutamine-hydrolyzing] subunit B / ATPPase subunit / GMP synthetase


Mass: 34609.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: guaAB, PH1347 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O59072, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30%(v/v) PEG400, 100mM Tris-HCl(pH 8.4), 200mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 60634 / Redundancy: 8.8 % / Rmerge(I) obs: 0.052
Reflection shellResolution: 1.79→1.85 Å / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.723 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24612 3071 5.1 %RANDOM
Rwork0.21002 ---
obs0.21182 57488 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.98 Å2 / Biso mean: 21.387 Å2 / Biso min: 7.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 0 276 4804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224612
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9726234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1335568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90223.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65715826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0781544
X-RAY DIFFRACTIONr_chiral_restr0.0980.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023462
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.22151
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23191
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9911.52955
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46324606
X-RAY DIFFRACTIONr_scbond_it2.56231885
X-RAY DIFFRACTIONr_scangle_it4.1494.51628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.786→1.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 223 -
Rwork0.249 4133 -
all-4356 -
obs--96.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1353-0.06640.07120.033-0.0240.3786-0.0149-0.0177-0.0133-0.00390.0241-0.0037-0.02080.0001-0.0092-0.0250.00320.0023-0.01450.00610.0035-2.803826.6475-2.0078
20.11320.03630.06560.01490.06450.6166-0.01420.0338-0.0226-0.0081-0.00540.0212-0.04030.00180.0196-0.00320.0028-0.0059-0.01210.0014-0.0177-11.363423.0006-47.7737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 308
2X-RAY DIFFRACTION2B1 - 308

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