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- PDB-1cli: X-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETA... -

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Basic information

Entry
Database: PDB / ID: 1cli
TitleX-RAY CRYSTAL STRUCTURE OF AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE (PURM), FROM THE E. COLI PURINE BIOSYNTHETIC PATHWAY, AT 2.5 A RESOLUTION
ComponentsPROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
KeywordsLIGASE / AIR SYNTHETASE / PURM / PURINE BIOSYNTHESIS / TRIFUNCTIONAL ENZYME / PURL / FGAR AMIDOTRANSFERASE / NOVEL FOLD
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLi, C. / Kappock, T.J. / Stubbe, J. / Weaver, T.M. / Ealick, S.E.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
Authors: Li, C. / Kappock, T.J. / Stubbe, J. / Weaver, T.M. / Ealick, S.E.
History
DepositionApr 28, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
C: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
D: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8208
Polymers147,4364
Non-polymers3844
Water9,062503
1
B: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
D: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9104
Polymers73,7182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
D: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9104
Polymers73,7182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-75 kcal/mol
Surface area24990 Å2
MethodPISA
3
A: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
B: PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9104
Polymers73,7182
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-75 kcal/mol
Surface area24950 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.170, 211.680, 94.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.6652, -0.2085, -0.717), (-0.1184, -0.9186, 0.377), (-0.7372, 0.3356, 0.5864)
Vector: 109.44, 190.67999, 7.33)

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Components

#1: Protein
PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE)


Mass: 36858.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SULFATE BINDNG / Source: (gene. exp.) Escherichia coli (E. coli) / Description: CLONED GENE / Cellular location: CYTOPLASM / Gene: PURM / Plasmid: PJS119 / Species (production host): Escherichia coli / Cell (production host): BL21 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Gene (production host): PURM / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P08178, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.4 Å3/Da / Density % sol: 47.5 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
215 mMTris-HCl1drop
310 mMdithiothreitol1drop
42.1-2.25 Mammonium sulfate1reservoir
53-6 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9792,0.9790,0.9638
DetectorType: ADSC / Detector: CCD / Date: Feb 1, 1998 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.9791
30.96381
ReflectionResolution: 2.5→20 Å / Num. obs: 44742 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 35.7 Å2 / Rsym value: 4.7 / Net I/σ(I): 8.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 14.3 / % possible all: 93
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.143

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Processing

Software
NameVersionClassification
SnBphasing
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2610 6 %RANDOM
Rwork0.192 ---
obs-43410 86.6 %-
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9990 0 20 503 10513
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.681.5
X-RAY DIFFRACTIONx_mcangle_it1.192
X-RAY DIFFRACTIONx_scbond_it0.972
X-RAY DIFFRACTIONx_scangle_it1.582.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 408 6 %
Rwork0.254 6387 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25

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