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- PDB-1z2l: Crystal structure of Allantoate-amidohydrolase from E.coli K12 in... -

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Basic information

Entry
Database: PDB / ID: 1z2l
TitleCrystal structure of Allantoate-amidohydrolase from E.coli K12 in complex with substrate Allantoate
ComponentsAllantoate amidohydrolase
KeywordsHYDROLASE / allantoate-amidohydrolase / allantoate / allC / purine catabolism / allantoin utilization / T1507 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


allantoate deiminase / allantoate deiminase activity / allantoin assimilation pathway / purine nucleobase metabolic process / manganese ion binding / protein homodimerization activity / zinc ion binding / cytoplasm
Similarity search - Function
Allantoate amidohydrolase / Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich ...Allantoate amidohydrolase / Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALLANTOATE ION / Allantoate amidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsAgarwal, R. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_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
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allantoate amidohydrolase
B: Allantoate amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8299
Polymers94,2002
Non-polymers6297
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-224 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.532, 186.579, 49.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Allantoate amidohydrolase


Mass: 47100.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: allC / Plasmid: TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: P77425, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1AL / ALLANTOATE ION / DIUREIDO-ACETATE


Mass: 175.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7N4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Peg 3350, Tris, Magnesium chloride, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9877, 0.9792, 0.94
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 2, 2005mirrors
ADSC QUANTUM 3152CCDDec 9, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GraphiteMADMx-ray1
2GraphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.98771
20.97921
30.941
41.11
ReflectionResolution: 2.25→50 Å / Num. all: 41530 / Num. obs: 41530 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Redundancy: 15.5 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.2
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 13 % / Rmerge(I) obs: 0.43 / Num. unique all: 4036 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MARMADdata reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→49.22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 593644.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1211 3 %RANDOM
Rwork0.229 ---
obs0.229 40329 94.3 %-
all-40329 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8151 Å2 / ksol: 0.323174 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.97 Å20 Å20 Å2
2---2.84 Å20 Å2
3----6.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 26 194 6625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 188 3 %
Rwork0.274 6061 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4XYZ.PARAM

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