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- PDB-1yny: Molecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Ev... -

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Basic information

Entry
Database: PDB / ID: 1yny
TitleMolecular Structure of D-Hydantoinase from a Bacillus sp. AR9: Evidence for mercury inhibition
ComponentsD-Hydantoinase
KeywordsHYDROLASE / TIM-barrel / hydantoinase / binuclear metal-binding
Function / homology
Function and homology information


dihydropyrimidinase / dihydropyrimidinase activity / metal ion binding / cytoplasm
Similarity search - Function
Hydantoinase/dihydropyrimidinase / 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 ...Hydantoinase/dihydropyrimidinase / 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 speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRadha Kishan, K.V. / Vohra, R.M. / Ganeshan, K. / Agrawal, V. / Sharma, V.M. / Sharma, R.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Molecular structure of D-hydantoinase from Bacillus sp. AR9: evidence for mercury inhibition.
Authors: Radha Kishan, K.V. / Vohra, R.M. / Ganesan, K. / Agrawal, V. / Sharma, V.M. / Sharma, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray diffraction analysis of a thermostable D-hydantoinase from mesophilic Bacillus sp.AR9
Authors: Agrawal, V. / Sharma, R. / Ganeshan, K. / Radha Kishan, K.V.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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: D-Hydantoinase
B: D-Hydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,1576
Polymers100,9382
Non-polymers2204
Water5,080282
1
A: D-Hydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5793
Polymers50,4691
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-Hydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5793
Polymers50,4691
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.540, 129.540, 102.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Cell settinghexagonal
Space group name H-MP64
DetailsThe asymmetric unit contains two molecules identified as chain A and B. Each molecule is independent and biologically active.

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Components

#1: Protein D-Hydantoinase / E.C.3.5.2.2 / Dihydropyrimidinase / DHPase


Mass: 50468.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: AR9 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5DLU2, dihydropyrimidinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.43 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, Cesium Chloride, imidazole, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 42440 / Num. obs: 42440 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.376 / Num. unique all: 4214 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Modified D-hydantoinase from Thermus sp. (PDB ID 1GKP)

1gkp


Resolution: 2.3→50 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: overall / Cross valid method: R-free / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2096 4.8 %random
Rwork0.199 ---
all-42440 --
obs-42440 97.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.708 Å2-1.368 Å20 Å2
2---0.708 Å20 Å2
3---1.416 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7047 0 4 282 7333
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.339
X-RAY DIFFRACTIONc_mcbond_it1.2841.5
X-RAY DIFFRACTIONc_mcangle_it2.0072
X-RAY DIFFRACTIONc_scbond_it2.1112
X-RAY DIFFRACTIONc_scangle_it3.0392.5

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