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- PDB-3oow: Octameric structure of the phosphoribosylaminoimidazole carboxyla... -

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Basic information

Entry
Database: PDB / ID: 3oow
TitleOctameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from Francisella tularensis subsp. tularensis SCHU S4.
ComponentsPhosphoribosylaminoimidazole carboxylase,catalytic subunit
KeywordsLYASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Phosphoribosylaminoimidazole carboxylase / Catalytic subunit / purE / Francisella tularensis subsp. tularensis SCHU S4 / Center for Structural Genomics of Infectious Diseases (CSGID)
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
FORMIC ACID / PHOSPHATE ION / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Octameric structure of the phosphoribosylaminoimidazole carboxylase catalytic subunit from Francisella tularensis subsp. tularensis SCHU S4.
Authors: Filippova, E.V. / Wawrzak, Z. / Kudritska, M. / Edwards, A. / Savchenko, A. / Anderson, F.W.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
B: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
C: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
D: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
E: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
F: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
G: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
H: Phosphoribosylaminoimidazole carboxylase,catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,69756
Polymers142,5158
Non-polymers3,18248
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42260 Å2
ΔGint-584 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.560, 96.300, 128.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Phosphoribosylaminoimidazole carboxylase,catalytic subunit


Mass: 17814.391 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: FTT_0896, purE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q5NGE9, phosphoribosylaminoimidazole carboxylase

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Non-polymers , 5 types, 593 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.92 Å3/Da / Density % sol: 36.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M NH4 Dihydrogen PO4, 0.1 M Tris, 6% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.75145 Å
DetectorType: MAR CCD / Detector: CCD / Date: Aug 13, 2010 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: MOLECULAR REPLACEMENT / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75145 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 110138 / Num. obs: 110138 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.54
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.38 / Num. unique all: 5387 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
CCP4model building
MrBUMPphasing
PHENIXmodel building
REFMAC5.5.0109refinement
XSCALEdata scaling
CCP4phasing
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: PDB entry 3OPQ

3opq


Resolution: 1.75→77.09 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.218 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 5493 5 %RANDOM
Rwork0.16833 ---
obs0.17016 104329 29.38 %-
all-104329 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--2.69 Å20 Å2
3----1.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→77.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9454 0 170 545 10169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229836
X-RAY DIFFRACTIONr_bond_other_d0.0010.026446
X-RAY DIFFRACTIONr_angle_refined_deg1.51.98313334
X-RAY DIFFRACTIONr_angle_other_deg0.962315919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15451303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6325.058344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.603151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6511540
X-RAY DIFFRACTIONr_chiral_restr0.090.21560
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110885
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021755
X-RAY DIFFRACTIONr_mcbond_it0.9541.56477
X-RAY DIFFRACTIONr_mcbond_other0.2761.52651
X-RAY DIFFRACTIONr_mcangle_it1.726210349
X-RAY DIFFRACTIONr_scbond_it3.15833359
X-RAY DIFFRACTIONr_scangle_it4.6254.52985
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 404 -
Rwork0.218 7643 -
obs--98.69 %
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)
10.2231-0.0959-0.0161-0.0140.02811.16090.02680.00560.08010.0372-0.0273-0.0082-0.0883-0.07850.00050.1285-0.00380.02550.1166-0.01040.15819.81867.3747102.0354
20.04670.06860.05180.07750.08870.86620.01230.01230.0148-0.03390.01170.0104-0.11230.0802-0.02410.1258-0.0310.01140.1318-0.01430.145568.097367.902592.43
31.03560.0234-0.08360.0315-0.07620.17320.04720.10.10660.0071-0.00520.0342-0.0523-0.0334-0.04210.14610.01690.00250.12570.01040.12239.205167.219872.8249
41.13960.1519-0.12020.02680.09670.2230.05310.1195-0.13680.03860.0052-0.04930.02510.0045-0.05840.13040.0124-0.01770.1277-0.02140.132745.822248.919472.6786
50.2121-0.1397-0.01920.06060.08150.9181-0.0115-0.0298-0.06460.03150.02150.00310.05330.0926-0.010.1103-0.0071-0.01760.1286-0.00210.157268.854349.845199.5753
60.90430.14690.23610.17030.14490.05790.0235-0.06050.11850.052-0.0411-0.03740.018-0.01360.01750.1685-0.0154-0.01510.1317-0.00760.100448.386367.7868121.2406
70.9297-0.0013-0.0860.0292-0.08540.11780.0505-0.0919-0.0878-0.0118-0.03480.03080.05590.0186-0.01560.1682-0.0247-0.00820.13310.01540.099741.448949.6643122.1379
80.17270.13940.05620.1053-0.0481.12570.02550.0346-0.0257-0.005-0.00340.00770.1048-0.0966-0.0220.1231-0.0099-0.00160.1217-0.0090.147219.37449.331895.1729
9-0.20460.00530.07170.43080.00670.6921-0.042-0.03010.0001-0.06510.01670.1771-0.0567-0.07640.02530.21860.00970.01120.00810.01180.200444.392158.768494.3914
100.29470.0908-0.05680.20750.0487-0.08480.07740.0111-0.0190.0117-0.0755-0.0019-0.0101-0.0106-0.00190.13630.0134-0.0060.1610.01580.078644.734958.720896.5202
114.2785-0.57869.7357-1.709-0.6550.6737-0.05560.00940.08520.0190.071-0.00080.2690.0017-0.01540.0779-0.04220.04930.3043-0.02360.099944.051958.549197.1588
120.89680.2641-0.08410.2999-0.02670.10160.0553-0.0190.00860.00870.00340.0001-0.0112-0.0168-0.05860.1150.0064-0.02230.14560.00770.064843.877858.589499.1206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 161
2X-RAY DIFFRACTION2B1 - 162
3X-RAY DIFFRACTION3C2 - 162
4X-RAY DIFFRACTION4D2 - 163
5X-RAY DIFFRACTION5E2 - 161
6X-RAY DIFFRACTION6F2 - 163
7X-RAY DIFFRACTION7G2 - 160
8X-RAY DIFFRACTION8H2 - 162
9X-RAY DIFFRACTION9E - H1 - 169
10X-RAY DIFFRACTION10A - F1 - 165
11X-RAY DIFFRACTION11F - G1 - 165
12X-RAY DIFFRACTION12A - C1 - 168

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