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- PDB-1yqc: Crystal Structure of Ureidoglycolate Hydrolase (AllA) from Escher... -

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Basic information

Entry
Database: PDB / ID: 1yqc
TitleCrystal Structure of Ureidoglycolate Hydrolase (AllA) from Escherichia coli O157:H7
ComponentsUreidoglycolate hydrolase
KeywordsHYDROLASE / AllA / Ureidoglycolate / Purine metabolism / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


ureidoglycolate lyase / ureidoglycolate lyase activity / ureidoglycolate hydrolase activity / allantoin catabolic process / purine nucleobase catabolic process
Similarity search - Function
Ureidoglycolate hydrolase / Ureidoglycolate lyase / Ureidoglycolate lyase, bacterial / Ureidoglycolate lyase domain superfamily / Ureidoglycolate lyase / RmlC-like cupin domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
GLYOXYLIC ACID / Ureidoglycolate lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.709 Å
AuthorsRaymond, S. / Tocilj, A. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Citation
Journal: Proteins / Year: 2005
Title: Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7
Authors: Raymond, S. / Tocilj, A. / Ajamian, E. / Li, Y. / Hung, M.-N. / Matte, A. / Cygler, M.
#1: Journal: METHODS ENZYMOL. / Year: 1997
Title: Processing of X-ray Diffraction Data Collected in Oscillation Mode
Authors: Otwinowski, Z. / Minor, W.
#2: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1999
Title: Automated MAD and MIR structure solution
Authors: Terwilliger, T.C. / Berendzen, J.
#3: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2000
Title: Maximum-likelihood density modification
Authors: Terwilliger, T.C.
#4: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 1997
Title: Refinement of macromolecular structures by the maximum-likelihood method
Authors: Murshudov, G.N.
History
DepositionFeb 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ureidoglycolate hydrolase
B: Ureidoglycolate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2433
Polymers39,1692
Non-polymers741
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-11 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.0470, 74.4660, 56.3640
Angle α, β, γ (deg.)90.0000, 103.8940, 90.0000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ureidoglycolate hydrolase /


Mass: 19584.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: AllA / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / References: UniProt: P63486, EC: 3.5.3.19
#2: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE, GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9611, 0.9800, 0.9802
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.981
30.98021
ReflectionResolution: 1.71→50 Å / Num. obs: 36248 / % possible obs: 96.2 %
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsDiffraction-ID
1.71-1.7799.50.37573111
1.77-1.841000.29273401
1.84-1.93990.19972941
1.93-2.031000.14274021
2.03-2.151000.10273951
2.15-2.32740.08954071
2.32-2.551000.06173591
2.55-2.921000.04273811
2.92-3.6892.30.03167741
3.68-5097.20.02771671

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Phasing

Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double primeF prime
1110.984.13-7.23
1120.98023.25-9.66
1130.96112.47-4.3
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1SE21.9150.1210.4990.2241.217
2SE21.5460.3550.5010.2121.128
3SE41.7990.3650.9740.2030.765
4SE49.8470.1580.9750.3640.868
5SE56.6850.0560.0420.3941.05
Phasing dmFOM : 0.67 / FOM acentric: 0.67 / FOM centric: 0.7 / Reflection: 22052 / Reflection acentric: 21213 / Reflection centric: 839
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-36.5120.890.890.841030925105
3.6-5.70.870.880.8228832723160
2.9-3.60.80.80.7538993741158
2.5-2.90.710.710.7339553818137
2.1-2.50.580.580.5859865813173
2-2.10.480.480.4842994193106

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.709→36.442 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.71 / ESU R: 0.143 / ESU R Free: 0.138 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1782 4.987 %RANDOM
Rwork0.2262 ---
all0.228 70830 --
obs0.228 35732 95.458 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.064 Å20 Å2-0.018 Å2
2--0.116 Å20 Å2
3----0.062 Å2
Refinement stepCycle: LAST / Resolution: 1.709→36.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 5 319 2878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212620
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9313568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35324.638138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34515420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3481516
X-RAY DIFFRACTIONr_chiral_restr0.1350.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022046
X-RAY DIFFRACTIONr_nbd_refined0.2330.21315
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.212
X-RAY DIFFRACTIONr_mcbond_it1.2761.51643
X-RAY DIFFRACTIONr_mcangle_it1.88822590
X-RAY DIFFRACTIONr_scbond_it2.76831090
X-RAY DIFFRACTIONr_scangle_it4.0914.5978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.709-1.7530.3331330.2972610276999.061
1.753-1.8010.3331210.2762549267499.85
1.801-1.8530.31160.262457257699.884
1.853-1.910.3761240.2982227255092.196
1.91-1.9730.3721220.2962148245292.577
1.973-2.0420.2711140.2222266238399.874
2.042-2.1180.2871040.22721802284100
2.118-2.2050.2351140.2252072222498.291
2.205-2.3020.365580.3251175213257.833
2.302-2.4140.278930.2281922202099.752
2.414-2.5440.275960.23318501946100
2.544-2.6980.299980.23117341832100
2.698-2.8830.256810.21716281709100
2.883-3.1120.292680.22115461614100
3.112-3.4070.261910.2113671458100
3.407-3.8040.277490.195967134875.371
3.804-4.3850.195640.1731128119899.499
4.385-5.3510.174710.1729361007100
5.351-7.4880.243440.216743787100
7.488-36.4420.339210.20144546999.36
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)
10.47160.3360.68650.46630.39361.6659-0.03620.0664-0.1539-0.10350.1043-0.0032-0.15820.061-0.0682-0.019-0.01280.0118-0.0316-0.0253-0.01347.077643.2011-0.4963
20.589-0.42770.80560.4037-0.34421.7243-0.0679-0.1182-0.1660.08970.1362-0.0136-0.1709-0.1496-0.0683-0.02140.01960.0141-0.01960.0316-0.01517.454843.225524.3596
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 160 / Label seq-ID: 1 - 160

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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