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- PDB-4e4t: Crystal structure of Phosphoribosylaminoimidazole carboxylase, AT... -

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Basic information

Entry
Database: PDB / ID: 4e4t
TitleCrystal structure of Phosphoribosylaminoimidazole carboxylase, ATPase subunit from Burkholderia ambifaria
ComponentsPhosphoribosylaminoimidazole carboxylase, ATPase subunit
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / purine biosynthesis / ATP binding / ACAIR / CAIR
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 28, 2012ID: 3UVZ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 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_ncs_dom_lim / 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_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_ref_seq_dif.details / _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: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
B: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3927
Polymers87,9122
Non-polymers4805
Water14,430801
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-72 kcal/mol
Surface area28990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.430, 73.390, 159.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 9 - 398 / Label seq-ID: 30 - 419

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Phosphoribosylaminoimidazole carboxylase, ATPase subunit /


Mass: 43955.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: MC40-6 / Gene: BamMC406_2543 / Production host: Escherichia coli (E. coli)
References: UniProt: B1YVV9, phosphoribosylaminoimidazole carboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BuamA.00036.a.A1 PS01234 at 46 mg/mL against Wiz3/4 condition H5, 20% PEG 8000, 0.1 M Hepes pH 7.5, 0.2 M ammonium sulfate, 10% isopropanol with 20% ethylene glycol as cryo-protectant, ...Details: BuamA.00036.a.A1 PS01234 at 46 mg/mL against Wiz3/4 condition H5, 20% PEG 8000, 0.1 M Hepes pH 7.5, 0.2 M ammonium sulfate, 10% isopropanol with 20% ethylene glycol as cryo-protectant, crystal tracking ID 228074h5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 111915 / Num. obs: 111431 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 24.671 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.590.4732.7433102815899.4
1.59-1.630.43.2733288795099.7
1.63-1.680.3044.2533250771799.9
1.68-1.730.245.4433389756599.9
1.73-1.790.1936.67330307325100
1.79-1.850.1647.9632666708499.9
1.85-1.920.12710.3532058682599.9
1.92-20.112.9731108659399.9
2-2.090.08315.7530187632999.9
2.09-2.190.0718.36290176067100
2.19-2.310.06120.8427593576499.9
2.31-2.450.05523.1726197547399.9
2.45-2.620.04925.6224553516899.9
2.62-2.830.04628.5522637481299.9
2.83-3.10.04231.2420385441199.7
3.1-3.470.03933.7918193403699.6
3.47-40.03635.3915586351998.3
4-4.90.03337.5213959299997.7
4.9-6.930.03136.4610882234197.2
6.930.02836.695754129591.5

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å46.22 Å
Translation3 Å46.22 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q2o

3q2o


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.1749 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8897 / SU B: 2.866 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0798 / SU Rfree: 0.0794 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 5586 5 %RANDOM
Rwork0.1772 ---
obs0.1785 111430 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.64 Å2 / Biso mean: 22.5074 Å2 / Biso min: 9.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5612 0 25 801 6438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195824
X-RAY DIFFRACTIONr_bond_other_d0.0040.023740
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9637984
X-RAY DIFFRACTIONr_angle_other_deg1.1139150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.455799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49823.537229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75215821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0671541
X-RAY DIFFRACTIONr_chiral_restr0.0840.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216723
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021158
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 382 -
Rwork0.244 7334 -
all-7716 -
obs--99.33 %
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)
10.07720.02190.08270.8119-0.05570.2946-0.0367-0.0078-0.0747-0.01820.00940.00130.00430.01910.02730.10160.0309-0.00160.1045-0.01830.1891-26.337-11.964-7.395
20.58230.306-0.36620.1891-0.19640.23540.0576-0.0777-0.0330.0857-0.06920.0127-0.02870.07110.01170.1727-0.00450.01120.1119-0.03050.1484-43.749-1.0411.985
31.3041-0.1317-0.23363.48440.60250.14210.05510.060.03670.0304-0.04460.11510.0023-0.0069-0.01040.1222-0.0151-0.01450.0738-0.02470.1843-57.151-3.9128.113
40.54-0.0141-0.1250.09330.04890.24860.02710.048-0.03360.0196-0.01820.0186-0.0429-0.0004-0.00890.10990.0158-0.01150.123-0.02430.1377-39.5686.276-10.477
51.3209-0.44590.45010.59740.37980.8337-0.01860.0781-0.14350.02860.0450.0051-0.00630.0261-0.02640.09250.0044-0.01240.1689-0.12060.1772-26.479-8.933-28.868
61.1564-1.0875-1.50351.91710.91572.24470.03710.2149-0.1489-0.1044-0.22370.0254-0.0264-0.18620.18660.0353-0.09060.08510.5929-0.49420.433-22.974-12.704-40.391
72.0489-1.2407-2.2960.75681.39832.59650.2995-0.04740.3417-0.15410.0526-0.205-0.2660.0184-0.35210.2039-0.06860.12230.2848-0.07050.1175-1.526.385-51.761
80.5427-0.03490.00290.06880.00210.29950.02690.082-0.0309-0.0310.0205-0.0851-0.0683-0.0275-0.04730.11760.0070.01650.1457-0.03950.1326-15.8368.765-29.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 95
2X-RAY DIFFRACTION2A96 - 150
3X-RAY DIFFRACTION3A151 - 193
4X-RAY DIFFRACTION4A194 - 398
5X-RAY DIFFRACTION5B9 - 57
6X-RAY DIFFRACTION6B58 - 107
7X-RAY DIFFRACTION7B108 - 198
8X-RAY DIFFRACTION8B199 - 398

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