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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 / homologyPhosphoribosylaminoimidazole carboxylase C-terminal domain / Rudiment single hybrid motif / ATP-grasp fold profile. / ATP-grasp domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, subdomain 1 / ATP-grasp fold / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / 5-(carboxyamino)imidazole ribonucleotide synthase activity ...Phosphoribosylaminoimidazole carboxylase C-terminal domain / Rudiment single hybrid motif / ATP-grasp fold profile. / ATP-grasp domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, subdomain 1 / ATP-grasp fold / Phosphoribosylaminoimidazole carboxylase, ATPase subunit / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / 5-(carboxyamino)imidazole ribonucleotide synthase activity / 5-(carboxyamino)imidazole ribonucleotide synthase / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol / N5-carboxyaminoimidazole ribonucleotide synthase
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.5 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 18, 1999 / Release: Nov 30, 1999
RevisionDateData content typeGroupProviderType
1.0Nov 30, 1999Structure modelrepositoryInitial release
1.1Apr 26, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Polyers158,1164
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
Polyers79,0582
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4660
ΔGint (kcal/M)-35
Surface area (Å2)27790
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
Polyers79,0582
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4590
ΔGint (kcal/M)-32
Surface area (Å2)27890
MethodPISA
Unit cell
γ
α
β
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-MP 1

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Components

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


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


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


Mass: 427.201 Da / Num. of mol.: 4 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Formula: H2O / Water

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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 / Density percent sol: 62 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: batch method
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: BRUKER AXS / Details: GOBEL MIRRORS / Detector: AREA DETECTOR / Collection date: Oct 1, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 2.5 Å / D resolution low: 3 Å / Number obs: 66345 / Observed criterion sigma I: 0 / Rmerge I obs: 0.072 / Rsym value: 0.72 / NetI over sigmaI: 12.6 / Redundancy: 1.8 % / Percent possible obs: 95.7
Reflection shellRmerge I obs: 0.181 / Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / MeanI over sigI obs: 2.1 / Rsym value: 0.181 / Redundancy: 1.3 % / Percent possible all: 89.6
Reflection shell
*PLUS
Percent possible obs: 89.6

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Processing

Software
NameVersionClassification
SAINTdata scaling
XCALIBREdata reduction
AMoREphasing
TNT5Drefinement
SAINTdata reduction
XCALIBREdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B6R
Sigma F: 0 / Stereochemistry target values: TNT PROTGEO
Solvent computationSolvent model details: TNT / Solvent model param bsol: 282.7 / Solvent model param ksol: 0.915
Least-squares processR factor R work: 0.185 / R factor all: 0.185 / Highest resolution: 2.5 Å / Lowest resolution: 3 Å / Number reflection obs: 66345 / Percent reflection obs: 95.7
Refine hist #LASTHighest resolution: 2.5 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 11029 / Nucleic acid: 0 / Ligand: 112 / Solvent: 491 / Total: 11632
Refine LS restraints
Refine IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013114340.600
X-RAY DIFFRACTIONt_angle_deg2.23154971.100
X-RAY DIFFRACTIONt_dihedral_angle_d19.27366380.000
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0062982.500
X-RAY DIFFRACTIONt_gen_planes0.01316403.50
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_deg19.30.000
X-RAY DIFFRACTIONt_plane_restr0.0133.5

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