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- PDB-2g3f: Crystal Structure of imidazolonepropionase complexed with imidazo... -

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Basic information

Entry
Database: PDB / ID: 2g3f
TitleCrystal Structure of imidazolonepropionase complexed with imidazole-4-acetic acid sodium salt, a substrate homologue
ComponentsImidazolonepropionase
KeywordsHYDROLASE / TIM BARREL
Function / homology
Function and homology information


imidazolonepropionase / imidazolonepropionase activity / L-histidine catabolic process / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / iron ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Imidazolonepropionase / 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 ...Imidazolonepropionase / 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
2H-IMIDAZOL-4-YLACETIC ACID / Imidazolonepropionase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, Y. / Liang, Y.H. / Su, X.D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: A catalytic mechanism revealed by the crystal structures of the imidazolonepropionase from Bacillus subtilis
Authors: Yu, Y. / Liang, Y.H. / Brostromer, E. / Quan, J.M. / Panjikar, S. / Dong, Y.H. / Su, X.D.
History
DepositionFeb 19, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: Imidazolonepropionase
B: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6156
Polymers91,2322
Non-polymers3834
Water7,296405
1
A: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8073
Polymers45,6161
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8073
Polymers45,6161
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Imidazolonepropionase
hetero molecules

B: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6156
Polymers91,2322
Non-polymers3834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area4790 Å2
ΔGint-104 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.530, 106.080, 66.310
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Imidazolonepropionase / Imidazolone-5-propionate hydrolase


Mass: 45615.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: hutI / Plasmid: pET-21-DEST / Production host: Escherichia coli (E. coli) / References: UniProt: P42084, imidazolonepropionase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IZC / 2H-IMIDAZOL-4-YLACETIC ACID / IMIDAZOLE-4-ACETIC ACID


Mass: 126.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 20%(w/v) PEG4000, 0.1M Tris-HCl pH7.5, 0.05M Imidazoli-4-acetic acid sodium salt, 2%(w/v) benzamidine hydrochloride, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Jan 12, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 53567 / Num. obs: 52978 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 7.7 Å2 / Rsym value: 0.067 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.31 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BB0

2bb0


Resolution: 2→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 17156.1 / 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
Rfree0.216 2060 4 %RANDOM
Rwork0.185 ---
all0.19 53663 --
obs0.187 50914 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4748 Å2 / ksol: 0.357525 e/Å3
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å21.28 Å2
2--2.23 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 20 405 6737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 320 4.1 %
Rwork0.21 7534 -
obs--88 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramiaa.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4iaa.paramwater_rep.top

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