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- PDB-4b4k: Crystal structure of Bacillus anthracis PurE -

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Basic information

Entry
Database: PDB / ID: 4b4k
TitleCrystal structure of Bacillus anthracis PurE
ComponentsN5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
KeywordsISOMERASE
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
N5-carboxyaminoimidazole ribonucleotide mutase / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionJul 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Other / Refinement description
Revision 1.2Feb 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
E: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
F: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
G: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
H: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
I: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
J: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
K: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
L: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE


Theoretical massNumber of molelcules
Total (without water)230,78412
Polymers230,78412
Non-polymers00
Water8,701483
1
A: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
B: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
C: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
D: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE

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


Theoretical massNumber of molelcules
Total (without water)153,8568
Polymers153,8568
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area29980 Å2
ΔGint-181.3 kcal/mol
Surface area38690 Å2
MethodPISA
2
E: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
F: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
G: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
H: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
I: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
J: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
K: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
L: N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE


Theoretical massNumber of molelcules
Total (without water)153,8568
Polymers153,8568
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29990 Å2
ΔGint-181.2 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.563, 151.904, 134.849
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19232.014 Da / Num. of mol.: 12
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, 5-(carboxyamino)imidazole ribonucleotide mutase, phosphoribosylaminoimidazole carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 36.08 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M CACODYLATE PH 6.5, 0.3-0.4M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2010 / Details: MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.5→47.07 Å / Num. obs: 56146 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.19
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 8.88 / % possible all: 89.5

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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: 2.5→47.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 18.26 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21712 2878 5.1 %RANDOM
Rwork0.18013 ---
obs0.18209 53163 93.07 %-
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: 44.672 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å20.27 Å2
2---0.68 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13945 0 0 483 14428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914161
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214052
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.98219187
X-RAY DIFFRACTIONr_angle_other_deg0.884332392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.11851870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.67524.682519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.901152442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5281572
X-RAY DIFFRACTIONr_chiral_restr0.0830.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115934
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022818
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
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 356 -
Rwork0.229 3918 -
obs--88.38 %
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)
12.7909-0.1775-1.17682.15420.41312.18660.01330.0137-0.15330.1906-0.08290.2303-0.035-0.29970.06960.032-0.00290.0130.1598-0.01960.038918.7409-28.51497.9356
22.20440.22130.10482.06260.3251.47050.03350.4513-0.0304-0.2694-0.04930.23-0.1204-0.38870.01580.06680.0636-0.03690.3016-0.02570.029819.1948-19.764-8.3252
33.728-0.6606-0.91031.8390.49942.0035-0.11220.4774-0.7746-0.2209-0.1539-0.02070.3501-0.08160.26610.1542-0.0170.03450.13-0.11940.263640.1633-48.5858-8.3752
43.22980.50130.11771.81470.4051.5860.1692-0.31640.42230.2214-0.07610.0425-0.393-0.0573-0.09320.2490.00670.05960.0938-0.0360.063739.40910.77928.1603
52.95230.0439-0.66511.81050.36291.7298-0.08320.1572-0.2797-0.07520.0285-0.03750.31360.12680.05470.13980.06-0.01230.0595-0.03750.041232.8524-37.470135.8455
61.94740.6645-0.1772.7347-0.62061.6950.0308-0.2958-0.26150.271-0.0389-0.11010.24620.25050.00810.14890.0828-0.02210.13180.02090.040340.2387-33.119652.2542
72.19-0.6761-0.69342.06140.21661.6529-0.0656-0.2472-0.22050.3113-0.00760.47030.2264-0.34450.07320.1336-0.05470.06440.20640.00030.18184.6539-30.221651.1481
81.7951-0.2645-0.17772.7712-0.66591.65510.08470.23870.1856-0.2582-0.0851-0.2828-0.21780.37280.00030.1227-0.04030.0360.19760.00360.047548.2248-5.204837.1617
92.00130.1062-0.09132.48070.57971.75450.0748-0.2550.2640.2128-0.11790.194-0.3262-0.19370.04310.20470.11950.02020.1701-0.04310.12698.41694.920752.1602
102.58750.11350.5281.60280.03791.9180.00230.29770.3415-0.2594-0.08560.1341-0.4361-0.27510.08330.31250.1278-0.01540.10880.02410.128115.99499.766736.1805
111.9956-0.29250.15313.29830.58181.98520.06090.2107-0.1956-0.3085-0.16530.51630.0855-0.41520.10440.0717-0.0002-0.05390.2542-0.0460.15491.6282-22.836134.6096
122.1963-0.50080.93141.8839-0.0562.1592-0.0563-0.13330.21110.23140.0768-0.1596-0.33890.289-0.02050.1596-0.0596-0.01010.1131-0.04130.060643.08622.39853.1913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 157
2X-RAY DIFFRACTION2B2 - 157
3X-RAY DIFFRACTION3C2 - 161
4X-RAY DIFFRACTION4D2 - 157
5X-RAY DIFFRACTION5I2 - 157
6X-RAY DIFFRACTION6J2 - 156
7X-RAY DIFFRACTION7K2 - 157
8X-RAY DIFFRACTION8L2 - 157
9X-RAY DIFFRACTION9E2 - 161
10X-RAY DIFFRACTION10F2 - 157
11X-RAY DIFFRACTION11G2 - 161
12X-RAY DIFFRACTION12H2 - 156

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