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- PDB-3e74: Crystal structure of E. coli allantoinase with iron ions at the m... -

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Basic information

Entry
Database: PDB / ID: 3.0E+74
TitleCrystal structure of E. coli allantoinase with iron ions at the metal center
ComponentsAllantoinase
KeywordsHYDROLASE / (beta/alpha)8-barrel domain / small beta-sheet domain / Metal-binding / Purine metabolism / Zinc
Function / homology
Function and homology information


allantoinase / allantoin assimilation pathway / allantoinase activity / purine nucleobase catabolic process / cobalt ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Allantoinase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel ...Allantoinase / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsKim, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of metal-dependent allantoinase from Escherichia coli
Authors: Kim, K. / Kim, M.I. / Chung, J. / Ahn, J.H. / Rhee, S.
History
DepositionAug 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Allantoinase
B: Allantoinase
C: Allantoinase
D: Allantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,85712
Polymers210,4104
Non-polymers4478
Water15,583865
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.681, 92.450, 168.430
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Allantoinase / / Allantoin-utilizing enzyme


Mass: 52602.523 Da / Num. of mol.: 4 / Mutation: V262I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: allB, glxB3, ybbX, b0512, JW0500 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77671, allantoinase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 3.09 Å3/Da / Density % sol: 60.21 % / Mosaicity: 0.607 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2.25M NaCl, 0.1M Na/K phosphate (pH6.7), 10mM EDTA, 1%(w/v) PEG3350, 1.2%(w/v) myo-inositol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 21, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 148374 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.114 / Χ2: 1.018
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.3 / Num. unique all: 14604 / Χ2: 0.49 / % possible all: 98.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 50 Å / FOM : 0.33 / Reflection: 85337
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se22.4530.67800.2470.451
2Se30.0030.7350.1120.3260.414
3Se27.010.6830.110.2780.415
4Se33.0650.6990.4950.1910.385
5Se24.9370.6190.4990.2030.269
6Se25.7590.2520.6480.1410.384
7Se35.5630.7080.4870.2260.476
8Se39.1170.6970.5980.2560.526
9Se37.4640.530.8940.3890.393
10Se22.3050.8670.5120.1520.284
11Se33.2230.7550.4860.1780.49
12Se28.160.5970.0920.2980.352
13Se37.90.5660.0530.3020.374
14Se30.9010.4120.7930.1370.391
15Se35.9470.4990.8870.410.382
16Se19.1820.360.9290.4170.309
17Se31.5350.2480.9230.3470.354
18Se42.6320.5920.0020.0060.247
19Se24.4640.420.7850.3580.373
20Se37.0690.8520.0960.3580.415
21Se40.3150.3580.6460.0750.395
22Se49.5070.4050.0770.50.444
23Se28.4510.6880.2660.4060.293
24Se33.0180.5270.690.1090.308
25Se36.9350.7110.3290.10.335
26Se28.8460.5860.5350.1980.238
27Se38.0590.4060.7360.0760.353
28Se42.1220.4120.6720.0820.319
29Se27.8420.6780.10.3130.263
30Se45.8750.7130.4560.1750.378
Phasing MAD shell
Resolution (Å)FOM Reflection
9.04-500.44059
5.69-9.040.447255
4.45-5.690.49300
3.77-4.450.3910928
3.33-3.770.3712259
3.01-3.330.3113231
2.77-3.010.2613945
2.58-2.770.214360
Phasing dmFOM : 0.71 / FOM acentric: 0.71 / FOM centric: 0.68 / Reflection: 85338 / Reflection acentric: 82356 / Reflection centric: 2982
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-42.4850.890.910.7538453462383
4.5-7.10.890.890.811184911201648
3.6-4.50.890.890.811478814211577
3.1-3.60.790.790.681475214310442
2.7-3.10.610.610.542529924680619
2.5-2.70.420.420.341480514492313

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.12phasing
RESOLVE2.12phasing
CNS1.1refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 26920 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 11882 7.9 %RANDOM
Rwork0.199 ---
obs-118552 79.3 %-
Solvent computationBsol: 61.118 Å2
Displacement parametersBiso max: 85.5 Å2 / Biso mean: 29.915 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-2.012 Å2
2--2.747 Å20 Å2
3----2.306 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13199 0 8 865 14072
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3591.5
X-RAY DIFFRACTIONc_scbond_it2.4672
X-RAY DIFFRACTIONc_mcangle_it2.1282
X-RAY DIFFRACTIONc_scangle_it3.4572.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4kcx_edit.param

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