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- PDB-1o59: Crystal structure of Allantoicase (yir029w) from Saccharomyces ce... -

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Basic information

Entry
Database: PDB / ID: 1o59
TitleCrystal structure of Allantoicase (yir029w) from Saccharomyces cerevisiae at 2.40 A resolution
ComponentsAllantoicase
KeywordsHYDROLASE / YIR029W / ALLANTOICASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


allantoicase / allantoicase activity / allantoin catabolic process / purine nucleobase metabolic process
Similarity search - Function
Allantoicase / Allantoicase domain / Allantoicase repeat / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution
Authors: Xu, Q. / Schwarzenbacher, R. / Page, R. / Sims, E. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / ...Authors: Xu, Q. / Schwarzenbacher, R. / Page, R. / Sims, E. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Cambell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Quijano, K. / Reyes, R. / Rezezadeh, F. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Allantoicase


Theoretical massNumber of molelcules
Total (without water)40,4651
Polymers40,4651
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.209, 107.209, 134.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

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Components

#1: Protein Allantoicase / Allantoate amidinohydrolase


Mass: 40464.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YIR029W / Production host: Escherichia coli (E. coli) / References: UniProt: P25335, allantoicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8756.81
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop, nanodrop30% Ethylene Glycol , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2932vapor diffusion, sitting drop, nanodrop30% Ethylene Glycol, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1reservoirpH7.8
2150 mM1reservoirNaCl
38 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL11-110.976224
SYNCHROTRONSSRL BL9-220.979608, 0.918370, 0.979413
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 17, 2003
ADSC QUANTUM 3152CCDApr 17, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystal Si(111) bent monochromatorSINGLE WAVELENGTHMx-ray1
2double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9762241
20.9796081
30.918371
40.9794131
ReflectionResolution: 2.4→54.554 Å / Num. all: 18532 / Num. obs: 18532 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 56.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1325 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 41.97 Å / Num. measured all: 94513
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→41.97 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.449 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.215
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. SELENIUM OCCUPANCIES WERE SET TO 0.5, TO REFLECT VARIABLE INCORPORATION DURING EXPRESSION. THIS VALUE MINIMIZES RFREE AND THE AMOUNT OF DIFFERENCE DENSITY OVER THE SITES. 2. RESIDUES 188- ...Details: 1. SELENIUM OCCUPANCIES WERE SET TO 0.5, TO REFLECT VARIABLE INCORPORATION DURING EXPRESSION. THIS VALUE MINIMIZES RFREE AND THE AMOUNT OF DIFFERENCE DENSITY OVER THE SITES. 2. RESIDUES 188-193 WERE OMITTED, BECAUSE THE STRONG DIFFERENCE DENSITY REMAINED AMBIGUOUS ABOUT THE PATH OF MAIN CHAIN TRACE; THE DENSITY WAS MODELED WITH WATER. 3. THE N-TERMINUS RETAINS STRONG DIFFERENCE DENSITY, SUGGESTING A DOUBLE CONFORMATION FOR MSE1; THIS PROVED DIFFICULT TO MODEL, SO THE CONFORMATION AGREEING BEST WITH EXPERIMENTAL DENSITY WAS RETAINED. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22238 830 4.5 %RANDOM
Rwork0.17542 ---
obs0.17765 17676 99.77 %-
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: 57.277 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å2-1.2 Å20 Å2
2---2.4 Å20 Å2
3---3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 0 218 2766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222633
X-RAY DIFFRACTIONr_bond_other_d0.0010.022362
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9133554
X-RAY DIFFRACTIONr_angle_other_deg0.83235478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3045312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26723.206131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73815446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9631520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02579
X-RAY DIFFRACTIONr_nbd_refined0.1850.2479
X-RAY DIFFRACTIONr_nbd_other0.1990.22422
X-RAY DIFFRACTIONr_nbtor_other0.0910.21648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0220.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.220
X-RAY DIFFRACTIONr_mcbond_it0.8321.51672
X-RAY DIFFRACTIONr_mcangle_it1.28522531
X-RAY DIFFRACTIONr_scbond_it1.70631201
X-RAY DIFFRACTIONr_scangle_it2.6034.51023
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.245 1323
Rfree-0
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)
13.39751.3062-0.59122.0648-0.61541.94520.0171-0.35830.42640.3071-0.16260.3068-0.1779-0.01220.1455-0.2430.01060.027-0.2104-0.093-0.290531.82353.28249.019
23.0547-0.3312-0.9744.775-0.79443.0036-0.0425-0.15060.08140.13980.17770.70010.073-0.0168-0.1352-0.37780.01830.0501-0.2744-0.0211-0.347815.88129.32446.217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
110 - 18712 - 199
22194 - 343206 - 355
Refinement
*PLUS
Num. reflection obs: 18506 / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.51

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