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- PDB-2bb0: Structure of Imidazolonepropionase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2bb0
TitleStructure of Imidazolonepropionase from Bacillus subtilis
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
ACETATE ION / Imidazolonepropionase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLiang, Y.H. / Yu, Y. / 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
DepositionOct 16, 2005Deposition 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 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: Imidazolonepropionase
B: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4816
Polymers91,2322
Non-polymers2494
Water9,584532
1
A: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7403
Polymers45,6161
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Imidazolonepropionase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7403
Polymers45,6161
Non-polymers1242
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)91,4816
Polymers91,2322
Non-polymers2494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4510 Å2
ΔGint-110 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.730, 106.340, 66.470
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Imidazolonepropionase / HutI / 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) / Plasmid: pET-21-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P42084, imidazolonepropionase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG4000, 0.1M Tris-HCl, 0.2M Sodium Acetate, 2% benzamidine hydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNumber: 54728 / Rmerge(I) obs: 0.098 / Χ2: 1.577 / D res high: 2 Å / D res low: 20 Å / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
5.392010010.0731.396
4.35.3910010.0672.661
3.764.310010.0672.224
3.423.7610010.0732.201
3.173.4210010.0831.926
2.993.1710010.0941.814
2.842.9999.710.1021.813
2.712.8499.710.1121.673
2.612.7199.810.1271.611
2.522.6199.710.1291.427
2.442.5299.710.1371.288
2.372.4499.710.1491.324
2.312.3799.710.1531.303
2.252.3199.710.1661.35
2.22.2599.910.1721.307
2.152.299.810.1841.271
2.112.1599.610.1951.254
2.072.1199.710.2121.22
2.032.0799.810.2311.147
22.0399.810.2561.082
ReflectionResolution: 2→20 Å / Num. all: 54837 / Num. obs: 54728 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.098 / Χ2: 1.577
Reflection shellResolution: 2→2.03 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.256 / Num. measured obs: 2690 / Χ2: 1.082 / % possible all: 99.8

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 88761
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.16-10039.70.725535
6.48-9.1648.40.7221050
5.29-6.48510.7081347
4.58-5.2940.70.7811615
4.1-4.5841.30.7791793
3.74-4.140.70.7851997
3.46-3.7441.50.7882162
3.24-3.4642.10.7732309
3.05-3.2445.30.7492459
2.9-3.0545.70.7542599
2.76-2.946.60.7392711
2.64-2.7647.60.7282889
2.54-2.6446.90.7282963
2.45-2.5446.20.7393108
2.36-2.4548.30.7093197
2.29-2.3649.80.7113333
2.22-2.2948.80.713389
2.16-2.2249.50.7233499
2.1-2.1648.80.7123655
2.05-2.148.70.7113699
2-2.05490.7033792
1.95-249.60.73912
1.91-1.9550.80.6863980
1.87-1.9152.10.6854046
1.83-1.8750.50.6754187
1.8-1.8352.80.6634194
1.76-1.851.10.6744350
1.73-1.7652.50.6714429
1.69-1.7355.30.5955562

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM4.2phasing
CNSrefinement
PDB_EXTRACT1.7data extraction
MAR345data collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 8239 7.7 %RANDOM
Rwork0.188 ---
all0.195 ---
obs0.191 54699 97.4 %-
Solvent computationBsol: 42.903 Å2
Displacement parametersBiso mean: 17.141 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20 Å2-0.802 Å2
2---7.969 Å20 Å2
3---5.639 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 10 532 6829
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3act.param
X-RAY DIFFRACTION4ion.param

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