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- PDB-4ay4: crystal structure of Bacillus anthracis PurE -

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Basic information

Entry
Database: PDB / ID: 4ay4
Titlecrystal structure of Bacillus anthracis PurE
ComponentsN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
KeywordsLYASE / ISOMERASE
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / lyase activity
Similarity search - Function
Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOliete, R. / Pous, J. / Rodriguez-Puente, S. / Abad-Zapatero, C. / Guasch, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Elastic and Inelastic Diffraction Changes Upon Variation of the Relative Humidity Environment of Pure Crystals
Authors: Oliete, R. / Pous, J. / Rodriguez-Puente, S. / Abad-Zapatero, C. / Guasch, A.
History
DepositionJun 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
B: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
C: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
D: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2239
Polymers76,9284
Non-polymers2955
Water6,575365
1
A: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
B: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
C: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
D: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
hetero molecules

A: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
B: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
C: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
D: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,44718
Polymers153,8568
Non-polymers59010
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area33200 Å2
ΔGint-187.3 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.003, 87.003, 270.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:

Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 1

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUAA2 - 15622 - 176
221GLUGLUBB2 - 15622 - 176
112GLYGLYAA2 - 15722 - 177
222GLYGLYCC2 - 15722 - 177
113GLUGLUAA2 - 15622 - 176
223GLUGLUDD2 - 15622 - 176

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999999, -0.000572, 0.001325), (-0.000678, 0.996658, -0.081689), (-0.001274, -0.08169, -0.996657)39.31008, 0.01214, 0.05994
3given(0.003043, -0.99893, 0.046154), (-0.999076, -0.005016, -0.042686), (0.042872, -0.045982, -0.998022)19.69598, 19.78328, -0.78426

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Components

#1: Protein
N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE / N5-CAIR MUTASE / PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE


Mass: 19232.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q81ZH8, UniProt: A0A6L7HA71*PLUS, phosphoribosylaminoimidazole carboxylase, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 1.92 Å3/Da / Density % sol: 35.9 % / Description: NONE
Crystal growpH: 8.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS PH8.5, 0.3M SODIUM ACETATE, 15% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2008 / Details: TOROIDAL MIRRORS
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42925 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 32.66
Reflection shellResolution: 2→2.07 Å / Redundancy: 6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.82 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMP

1xmp


Resolution: 2→43.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.778 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.17988 2063 5.1 %RANDOM
Rwork0.14729 ---
obs0.14893 38506 96.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.42 Å20 Å2
2---0.42 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4682 0 20 365 5067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194794
X-RAY DIFFRACTIONr_bond_other_d0.0030.024755
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9856493
X-RAY DIFFRACTIONr_angle_other_deg0.976310961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94824.773176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73315828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3561524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215415
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02953
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.87

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A13871.01
12B13871.01
21A13911.15
22C13911.15
31A13841.39
32D13841.39
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 135 -
Rwork0.162 2698 -
obs--93.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.99440.34950.39931.38150.41771.29750.0023-0.20670.22240.16410.00020.0343-0.1554-0.0238-0.00240.05650.00650.0110.0356-0.01210.036615.364525.28367.1162
21.9351-0.40040.37431.3783-0.56231.3396-0.00460.15380.1761-0.0873-0.01370.0213-0.1180.01570.01820.0332-0.00530.00050.02270.01450.02623.325824.4276-9.3167
31.64170.46290.48051.99220.30751.1966-0.01250.14520.0168-0.16440.02720.1613-0.0047-0.0947-0.01470.01530.005-0.01250.07080.01410.0166-5.20663.9378-8.2831
41.3775-0.29790.52542.2042-0.31021.2704-0.0062-0.1485-0.03580.19660.009-0.1710.00580.1362-0.00290.0193-0.0015-0.01480.08790.0060.029944.39093.86028.3047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 157
2X-RAY DIFFRACTION2B2 - 160
3X-RAY DIFFRACTION3C2 - 157
4X-RAY DIFFRACTION4D1 - 161

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