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- PDB-3k5h: Crystal structure of carboxyaminoimidazole ribonucleotide synthas... -

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Basic information

Entry
Database: PDB / ID: 3k5h
TitleCrystal structure of carboxyaminoimidazole ribonucleotide synthase from asperigillus clavatus complexed with ATP
ComponentsPhosphoribosyl-aminoimidazole carboxylase
KeywordsLYASE / purine biosynthesis / ATP-grasp
Function / homology
Function and homology information


phosphoribosylaminoimidazole carboxylase / 5-amino-4-imidazole carboxylate lyase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, fungi/plant / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Class I PurE / PurE domain / AIR carboxylase / AIR carboxylase ...Phosphoribosylaminoimidazole carboxylase, fungi/plant / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Class I PurE / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Phosphoribosylaminoimidazole carboxylase
Similarity search - Component
Biological speciesAspergillus clavatus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsThoden, J.B. / Holden, H.M. / Paritala, H. / Firestine, S.M.
CitationJournal: Biochemistry / Year: 2010
Title: Structural and functional studies of Aspergillus clavatus N(5)-carboxyaminoimidazole ribonucleotide synthetase
Authors: Thoden, J.B. / Holden, H.M. / Paritala, H. / Firestine, S.M.
History
DepositionOct 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosyl-aminoimidazole carboxylase
B: Phosphoribosyl-aminoimidazole carboxylase
C: Phosphoribosyl-aminoimidazole carboxylase
D: Phosphoribosyl-aminoimidazole carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,10716
Polymers178,8834
Non-polymers2,22312
Water15,295849
1
A: Phosphoribosyl-aminoimidazole carboxylase
B: Phosphoribosyl-aminoimidazole carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5538
Polymers89,4422
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-2 kcal/mol
Surface area28660 Å2
MethodPISA
2
C: Phosphoribosyl-aminoimidazole carboxylase
D: Phosphoribosyl-aminoimidazole carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5538
Polymers89,4422
Non-polymers1,1126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-3 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.900, 134.400, 99.600
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoribosyl-aminoimidazole carboxylase


Mass: 44720.836 Da / Num. of mol.: 4 / Fragment: residues 1-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus clavatus (mold) / Strain: NRRL 1 / Gene: ACLA_051590, ade2 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettas(DE2)
References: UniProt: A1CII2, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 849 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18% PEG-5000 monomethylether, 10 mM ATP, 40 mM MgCl2, 200 mM NaCl, 100mM CHES, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 14, 2009 / Details: montel
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 104348 / Num. obs: 104348 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.2 / Num. unique all: 12740 / Rsym value: 0.309 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: non-published structure (in-house) from yeast

Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 10331 -random
Rwork0.196 ---
all0.198 104194 --
obs0.198 104194 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11869 0 132 849 12850

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