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- PDB-1b6s: STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE -

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Basic information

Entry
Database: PDB / ID: 1b6s
TitleSTRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE
ComponentsPROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
KeywordsLYASE / ATP-GRASP / CARBOXYPHOSPHATE / PURINE BIOSYNTHESIS
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / 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'-DIPHOSPHATE / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
CitationJournal: Biochemistry / Year: 1999
Title: Three-dimensional structure of N5-carboxyaminoimidazole ribonucleotide synthetase: a member of the ATP grasp protein superfamily.
Authors: Thoden, J.B. / Kappock, T.J. / Stubbe, J. / Holden, H.M.
History
DepositionJan 18, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
B: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
C: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
D: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,92212
Polymers158,1164
Non-polymers1,8068
Water8,845491
1
A: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
B: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9616
Polymers79,0582
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-35 kcal/mol
Surface area27790 Å2
MethodPISA
2
C: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
D: PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9616
Polymers79,0582
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-32 kcal/mol
Surface area27890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.600, 92.100, 102.600
Angle α, β, γ (deg.)66.10, 82.70, 81.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PROTEIN (N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE) / AIRC / PURK


Mass: 39528.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P09029, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
2100 mMHEPES11
3125 mM11KCl
45.0 mM11MgCl2
55 mMAMP-PNP11
68-17 %(w/v)PEG11

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER AXS / Detector: AREA DETECTOR / Date: Oct 1, 1998 / Details: GOBEL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 66345 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.072 / Rsym value: 0.72 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.181 / % possible all: 89.6
Reflection shell
*PLUS
% possible obs: 89.6 %

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Processing

Software
NameVersionClassification
SAINTdata scaling
XCALIBREdata reduction
AMoREphasing
TNT5Drefinement
SAINTdata reduction
XCALIBREdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B6R

1b6r


Resolution: 2.5→30 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.185 --
all0.185 --
obs-66345 95.7 %
Solvent computationSolvent model: TNT / Bsol: 282.7 Å2 / ksol: 0.915 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11029 0 112 491 11632
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013114340.6
X-RAY DIFFRACTIONt_angle_deg2.23154971.1
X-RAY DIFFRACTIONt_dihedral_angle_d19.27366380
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0062982.5
X-RAY DIFFRACTIONt_gen_planes0.01316403.5
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.009213
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg19.30
X-RAY DIFFRACTIONt_plane_restr0.0133.5

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