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- PDB-1pkx: Crystal Structure of human ATIC in complex with XMP -

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Basic information

Entry
Database: PDB / ID: 1pkx
TitleCrystal Structure of human ATIC in complex with XMP
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / ATIC / AICAR transformylase / IMP Cyclohydrolase / xanthosine monophosphate / purine biosynthesis
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 ...phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 / 'de novo' IMP biosynthetic process / nucleobase-containing compound metabolic process / dihydrofolate metabolic process / animal organ regeneration / tetrahydrofolate biosynthetic process / cerebellum development / cerebral cortex development / Signaling by ALK fusions and activated point mutants / cadherin binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily ...Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / XANTHOSINE-5'-MONOPHOSPHATE / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWolan, D.W. / Cheong, C.G. / Greasley, S.E. / Wilson, I.A.
CitationJournal: Biochemistry / Year: 2004
Title: Structural Insights into the Human and Avian IMP Cyclohydrolase Mechanism via Crystal Structures with the Bound XMP Inhibitor.
Authors: Wolan, D.W. / Cheong, C.G. / Greasley, S.E. / Wilson, I.A.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
C: Bifunctional purine biosynthesis protein PURH
D: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,66210
Polymers258,7754
Non-polymers8876
Water17,601977
1
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8315
Polymers129,3872
Non-polymers4433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-65 kcal/mol
Surface area43320 Å2
MethodPISA
2
C: Bifunctional purine biosynthesis protein PURH
D: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8315
Polymers129,3872
Non-polymers4433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12340 Å2
ΔGint-70 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.520, 93.560, 179.880
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is a homodimer and AU contains two dimers

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Components

#1: Protein
Bifunctional purine biosynthesis protein PURH / ATIC


Mass: 64693.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase) and IMP cyclohydrolase (Inosinicase) (IMP synthetase)
Source: (gene. exp.) Homo sapiens (human) / Gene: ATIC / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3
References: UniProt: P31939, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 977 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Polyethylene glycol 3000, pH 7.5-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / PH range low: 8 / PH range high: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
215-17 %PEG30001reservoir
30.1 MTris-HCl1reservoirpH7.5-8.0
45 %MPD1reservoir
56 mMdithiothreitol1reservoir
60.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 177135 / % possible obs: 87.7 % / Redundancy: 2.1 % / Rsym value: 0.053 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.394 / % possible all: 47.8
Reflection
*PLUS
Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 47.8 % / Num. unique obs: 9598 / Rmerge(I) obs: 0.394

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Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G8M

1g8m


Resolution: 1.9→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 8496 random 5 %
Rwork0.211 --
obs-160871 -
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17762 0 52 977 18791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.39
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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