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- PDB-6jp9: Crsytal structure of a XMP complexed ATPPase subunit of M. jannas... -

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Basic information

Entry
Database: PDB / ID: 6jp9
TitleCrsytal structure of a XMP complexed ATPPase subunit of M. jannaschii GMP synthetase
ComponentsGMP synthase [glutamine-hydrolyzing] subunit B
KeywordsLIGASE / Purine biosynthesis / Methanocaldococcus jannaschii / GMP synthetase / ATP pyrophosphatase / P-loop
Function / homology
Function and homology information


GMP synthase activity / GMP synthase (glutamine-hydrolysing) / pyrophosphatase activity / GMP biosynthetic process / 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
MALONIC ACID / TRIETHYLENE GLYCOL / XANTHOSINE-5'-MONOPHOSPHATE / GMP synthase [glutamine-hydrolyzing] subunit B
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShivakumarasamy, S. / Balaram, H.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (India) India
Department of Biotechnology (India) India
CitationJournal: Biochemistry / Year: 2022
Title: Mechanistic Insights into the Functioning of a Two-Subunit GMP Synthetase, an Allosterically Regulated, Ammonia Channeling Enzyme.
Authors: Shivakumaraswamy, S. / Kumar, S. / Bellur, A. / Polisetty, S.D. / Balaram, H.
History
DepositionMar 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: GMP synthase [glutamine-hydrolyzing] subunit B
D: GMP synthase [glutamine-hydrolyzing] subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,14010
Polymers139,4254
Non-polymers1,7156
Water5,585310
1
A: GMP synthase [glutamine-hydrolyzing] subunit B
B: GMP synthase [glutamine-hydrolyzing] subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4434
Polymers69,7132
Non-polymers7302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-21 kcal/mol
Surface area25270 Å2
MethodPISA
2
C: GMP synthase [glutamine-hydrolyzing] subunit B
D: GMP synthase [glutamine-hydrolyzing] subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6976
Polymers69,7132
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-31 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.180, 100.430, 157.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34856.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Strain: DSM 2661 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q58531, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE / Xanthosine monophosphate


Mass: 365.213 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 294.15 K / Method: microbatch / pH: 5.5
Details: 2 micro liters of 18 mg/ml protein solution containing 1 mM XMP, 1 mM PPi, 20 mM MgCl2 was mixed with an equal volume of crystallization condition containing 20 % (w/v) PEG 1500 and 0.1 M MIB buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→52.53 Å / Num. obs: 76858 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 32.1 Å2 / CC1/2: 0.989 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4500 / CC1/2: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPL

2dpl


Resolution: 2.1→52.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: FREE R-VALUE / ESU R: 0.238 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27316 3815 5 %RANDOM
Rwork0.22112 ---
obs0.22372 72806 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.396 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å2-0 Å20 Å2
2--0.25 Å2-0 Å2
3----1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→52.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8747 0 113 310 9170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198997
X-RAY DIFFRACTIONr_bond_other_d00.028530
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.99412228
X-RAY DIFFRACTIONr_angle_other_deg3.8319651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4551151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32424.473351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.494151490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1771556
X-RAY DIFFRACTIONr_chiral_restr0.10.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219914
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7564.6454649
X-RAY DIFFRACTIONr_mcbond_other3.7564.6454648
X-RAY DIFFRACTIONr_mcangle_it5.2696.9345785
X-RAY DIFFRACTIONr_mcangle_other5.2696.9345786
X-RAY DIFFRACTIONr_scbond_it4.1064.7054348
X-RAY DIFFRACTIONr_scbond_other4.1014.7054346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0026.9626443
X-RAY DIFFRACTIONr_long_range_B_refined8.0854.119664
X-RAY DIFFRACTIONr_long_range_B_other8.08254.1099653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 290 -
Rwork0.296 5292 -
obs--99.98 %

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