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- PDB-2imo: Crystal structure of allantoate amidohydrolase from Escherichia c... -

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Basic information

Entry
Database: PDB / ID: 2imo
TitleCrystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6
ComponentsAllantoate amidohydrolase
KeywordsHYDROLASE / allantoate amidohydrolase / apoenzyme / allC / T1507 / Structural Genomics / PSI-2 / 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 amidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / 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
DepositionOct 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Allantoate amidohydrolase
B: Allantoate amidohydrolase


Theoretical massNumber of molelcules
Total (without water)95,5132
Polymers95,5132
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-27 kcal/mol
Surface area29460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.747, 183.923, 48.777
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: 47756.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: allC_ecoli / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P77425, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.05 M KH2PO4, 20%PEG8000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9877,0.9792,0.94
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2004 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98771
20.97921
30.941
ReflectionResolution: 2.8→50 Å / Num. all: 19631 / Num. obs: 19631 / % possible obs: 98 % / Observed criterion σ(F): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 1501 / % possible all: 84.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→48.78 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 105623.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The missing residues listed in Remark 465 are due to lack of or weak electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.302 578 2.9 %RANDOM
Rwork0.245 ---
obs0.245 19631 90 %-
all-19631 --
Solvent computationBsol: 61.0507 Å2 / ksol: 0.399288 e/Å3
Displacement parametersBiso mean: 53.9 Å2
Baniso -1Baniso -2Baniso -3
1-19.76 Å20 Å20 Å2
2--0.6 Å20 Å2
3----20.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6208 0 0 57 6265
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 55 2.3 %
Rwork0.409 2348 -
obs--67.6 %
Xplor file
Refine-IDSerial noTopol file
X-RAY DIFFRACTION1protein.top
X-RAY DIFFRACTION2xyz.top

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