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- PDB-4j0n: Crystal structure of a manganese dependent isatin hydrolase -

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Basic information

Entry
Database: PDB / ID: 4j0n
TitleCrystal structure of a manganese dependent isatin hydrolase
ComponentsIsatin hydrolase B
KeywordsHYDROLASE / Manganese binding
Function / homology
Function and homology information


isatin hydrolase / arylformamidase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / tryptophan catabolic process to kynurenine / manganese ion binding
Similarity search - Function
Putative cyclase / Kynurenine formamidase/cyclase-like / Kynurenine formamidase superfamily / Putative cyclase / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Isatin hydrolase
Similarity search - Component
Biological speciesLabrenzia aggregata IAM 12614 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBjerregaard-Andersen, K. / Sommer, T. / Jensen, J.K. / Jochimsen, B. / Etzerodt, M. / Morth, J.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A proton wire and water channel revealed in the crystal structure of isatin hydrolase.
Authors: Bjerregaard-Andersen, K. / Sommer, T. / Jensen, J.K. / Jochimsen, B. / Etzerodt, M. / Morth, J.P.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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: Isatin hydrolase B
B: Isatin hydrolase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3828
Polymers56,1632
Non-polymers2196
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-108 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 51.940, 176.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Isatin hydrolase B


Mass: 28081.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Labrenzia aggregata IAM 12614 (bacteria)
Gene: SIAM614_09648 / Production host: Escherichia coli (E. coli) / References: UniProt: A0NLY7
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18% PEG3350, 0.2M Calcium acetate, 0.5 mM Manganese(II) chloride, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.3 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2011 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator, first crystal indirectly water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.25→43.59 Å / Num. all: 50648 / Num. obs: 50263 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 29.65 Å2 / Net I/σ(I): 11.12

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX(phenix.phaser: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
xia2(xia2-0.3.5.0)data reduction
xia2(xia2-0.3.5.0)data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R61

1r61


Resolution: 2.25→43.59 Å / SU ML: 0.3 / σ(F): 1.07 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2557 5.1 %Random
Rwork0.1705 ---
obs0.173 50165 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 6 286 4220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084036
X-RAY DIFFRACTIONf_angle_d1.0425508
X-RAY DIFFRACTIONf_dihedral_angle_d13.211438
X-RAY DIFFRACTIONf_chiral_restr0.07604
X-RAY DIFFRACTIONf_plane_restr0.005726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.29350.3621460.28952478X-RAY DIFFRACTION96
2.2935-2.34030.32761550.27052679X-RAY DIFFRACTION100
2.3403-2.39120.32121430.24122654X-RAY DIFFRACTION99
2.3912-2.44680.28371500.23292657X-RAY DIFFRACTION100
2.4468-2.5080.27441640.24192622X-RAY DIFFRACTION100
2.508-2.57580.23931420.22562699X-RAY DIFFRACTION100
2.5758-2.65160.23531330.2092590X-RAY DIFFRACTION100
2.6516-2.73720.26071620.19242751X-RAY DIFFRACTION99
2.7372-2.8350.24581600.19762560X-RAY DIFFRACTION99
2.835-2.94850.23571300.18622624X-RAY DIFFRACTION100
2.9485-3.08260.28191740.18432649X-RAY DIFFRACTION99
3.0826-3.24510.26261370.16682719X-RAY DIFFRACTION100
3.2451-3.44830.19281590.16282657X-RAY DIFFRACTION99
3.4483-3.71450.22031140.14272664X-RAY DIFFRACTION99
3.7145-4.0880.20791140.13812630X-RAY DIFFRACTION99
4.088-4.6790.12471350.1142635X-RAY DIFFRACTION98
4.679-5.89270.18231230.13152668X-RAY DIFFRACTION100
5.8927-43.59910.17981160.15862672X-RAY DIFFRACTION99

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