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- PDB-3trh: Structure of a phosphoribosylaminoimidazole carboxylase catalytic... -

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Basic information

Entry
Database: PDB / ID: 3trh
TitleStructure of a phosphoribosylaminoimidazole carboxylase catalytic subunit (purE) from Coxiella burnetii
ComponentsPhosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
KeywordsLYASE / Purines / pyrimidines / nucleosides / nucleotides
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
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
B: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
C: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
D: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
E: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
F: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
G: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
H: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
I: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
J: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
K: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
L: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
M: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
N: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
O: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
P: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit


Theoretical massNumber of molelcules
Total (without water)283,38816
Polymers283,38816
Non-polymers00
Water12,791710
1
A: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
B: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
C: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
D: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
E: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
F: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
I: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
K: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit


Theoretical massNumber of molelcules
Total (without water)141,6948
Polymers141,6948
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30370 Å2
ΔGint-200 kcal/mol
Surface area42760 Å2
MethodPISA
2
G: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
H: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
J: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
L: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
M: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
N: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
O: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit
P: Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit


Theoretical massNumber of molelcules
Total (without water)141,6948
Polymers141,6948
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30200 Å2
ΔGint-200 kcal/mol
Surface area42560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.266, 96.292, 152.724
Angle α, β, γ (deg.)90.000, 91.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoribosylaminoimidazole carboxylase carboxyltransferase subunit


Mass: 17711.721 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_2002, purE / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83AA3, phosphoribosylaminoimidazole carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium formate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 126961 / Num. obs: 122264 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.095 / Χ2: 1.134 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.242.40.4757500.611191.2
2.24-2.282.50.4860420.788195
2.28-2.322.70.48360770.582197.3
2.32-2.372.80.45162090.58197.9
2.37-2.422.90.3762510.603198.3
2.42-2.4830.33462010.622198.3
2.48-2.5430.31362610.617198.4
2.54-2.6130.25461930.669198.1
2.61-2.6930.22561700.736197.9
2.69-2.7730.19961830.765197.8
2.77-2.8730.17161820.837197.5
2.87-2.9930.14861340.917196.8
2.99-3.1230.11761261.116196.6
3.12-3.2930.09860831.318196
3.29-3.4930.07960501.607195.1
3.49-3.7630.06760131.656194.4
3.76-4.1430.05859791.602193.4
4.14-4.743.10.05459691.792193.9
4.74-5.973.20.05562481.961197.4
5.97-503.40.05961432.581193.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.203→40.802 Å / Occupancy max: 1 / Occupancy min: 0.53 / FOM work R set: 0.8474 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 6139 5.02 %RANDOM
Rwork0.1908 ---
all0.1928 134117 --
obs0.1928 122225 95.71 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.669 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 116.12 Å2 / Biso mean: 39.1083 Å2 / Biso min: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1--4.0573 Å2-0 Å2-2.2202 Å2
2---4.1357 Å20 Å2
3---8.193 Å2
Refinement stepCycle: LAST / Resolution: 2.203→40.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18980 0 0 710 19690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419204
X-RAY DIFFRACTIONf_angle_d0.77326004
X-RAY DIFFRACTIONf_chiral_restr0.0493231
X-RAY DIFFRACTIONf_plane_restr0.0033345
X-RAY DIFFRACTIONf_dihedral_angle_d13.1366966
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.203-2.22830.32021750.26123078325377
2.2283-2.25450.2991980.25333714391292
2.2545-2.2820.30182090.24033835404495
2.282-2.31090.32351930.25223849404296
2.3109-2.34130.28412190.24463931415098
2.3413-2.37340.3052030.23543921412498
2.3734-2.40730.25612350.22353997423299
2.4073-2.44320.24711920.21553932412498
2.4432-2.48140.2911880.20813990417899
2.4814-2.52210.25082200.21993916413698
2.5221-2.56550.2572090.22053925413498
2.5655-2.61220.27162250.19643987421299
2.6122-2.66240.24542090.19963921413098
2.6624-2.71680.29222130.20723952416598
2.7168-2.77580.26822230.21573930415398
2.7758-2.84040.26782080.20893929413798
2.8404-2.91140.28562060.20813933413997
2.9114-2.99010.22152110.21013908411997
2.9901-3.0780.25311970.19743900409797
3.078-3.17740.24262170.1983885410296
3.1774-3.29090.23132030.19413841404496
3.2909-3.42260.23442190.1853883410295
3.4226-3.57820.22121840.18963845402995
3.5782-3.76680.22472090.18043817402694
3.7668-4.00260.19421860.16333800398693
4.0026-4.31130.19752160.15793787400393
4.3113-4.74460.17042030.15363803400694
4.7446-5.42980.17961830.15383964414796
5.4298-6.83570.21211940.20841124306100
6.8357-40.80860.20071920.16813801399391

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