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- PDB-2vpi: Human GMP synthetase - glutaminase domain -

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Basic information

Entry
Database: PDB / ID: 2vpi
TitleHuman GMP synthetase - glutaminase domain
ComponentsGMP SYNTHASE
KeywordsLIGASE / GUANINE MONOPHOSPHATE SYNTHETASE / PHOSPHOPROTEIN / GMP SYNTHETASE / GMP BIOSYNTHESIS / GLUTAMINE AMIDOTRANSFERASE / GMPS / CYTOPLASM / ATP-BINDING / PROTO-ONCOGENE / GLUTAMINASE DOMAIN / NUCLEOTIDE-BINDING / PURINE BIOSYNTHESIS / CHROMOSOMAL REARRANGEMENT
Function / homology
Function and homology information


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase activity / GMP synthase (glutamine-hydrolysing) / purine ribonucleoside monophosphate biosynthetic process / purine nucleobase biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / GMP biosynthetic process / Azathioprine ADME / glutamine metabolic process / ATP binding / cytosol
Similarity search - Function
GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. ...GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWelin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Van Der Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Gmp Synthetase - Glutaminase Domain
Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, ...Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P.
History
DepositionFeb 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)47,6382
Polymers47,6382
Non-polymers00
Water1,802100
1
A: GMP SYNTHASE


Theoretical massNumber of molelcules
Total (without water)23,8191
Polymers23,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GMP SYNTHASE


Theoretical massNumber of molelcules
Total (without water)23,8191
Polymers23,8191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.680, 120.880, 47.320
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA24 - 5423 - 53
21METMETILEILEBB24 - 5423 - 53
12ILEILEVALVALAA64 - 12363 - 122
22ILEILEVALVALBB64 - 12363 - 122
13GLUGLULEULEUAA125 - 139124 - 138
23GLUGLULEULEUBB125 - 139124 - 138
14LEULEUVALVALAA143 - 219142 - 218
24LEULEUVALVALBB143 - 219142 - 218

NCS oper: (Code: given
Matrix: (0.8458, -0.03098, 0.5326), (-0.02708, -0.9995, -0.01513), (0.5328, -0.00162, -0.8463)
Vector: -6.039, 31.35, 22.54)

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Components

#1: Protein GMP SYNTHASE / GLUTAMINE AMIDOTRANSFERASE / GMP SYNTHETASE


Mass: 23819.168 Da / Num. of mol.: 2 / Fragment: GLUTAMINASE DOMAIN, RESIDUES 25-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 PRARE
References: UniProt: P49915, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS AN N-TERMINAL HEXAHISTIDINE TAG MHHHHHHSSGVDLGTENLYFQSM

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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: 2.38 Å3/Da / Density % sol: 40.11 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M AMMONIUM ACETATE 0.1 M BIS-TRIS PH 5.5 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 14466 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.13 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.52
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.96 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPM

1gpm


Resolution: 2.4→19.77 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.854 / SU B: 8.472 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 77-85 IN CHAIN A AND 77-86 IN CHAIN B ARE DISORDERED. MET 24 IS FROM HIS TAG AND CORRESPONDS TO A TYR IN BIOLOGICAL SEQUENCE.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 733 5.1 %RANDOM
Rwork0.203 ---
obs0.206 13703 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.61 Å2
2---0.37 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 0 100 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9613900
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26924.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05315502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6291514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022152
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.21189
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21978
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.551.51893
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.95422956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.51631107
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.554.5942
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1312 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.070.5
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 60
Rwork0.245 951

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