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- PDB-5nna: Isatin hydrolase A (IHA) from Labrenzia aggregata bound to benzyl... -

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Basic information

Entry
Database: PDB / ID: 5nna
TitleIsatin hydrolase A (IHA) from Labrenzia aggregata bound to benzyl benzoate
Componentsisatin hydrolase A
KeywordsHYDROLASE / Isatin / Labrenzia aggregata / benzyl benzoate
Function / homology
Function and homology information


arylformamidase activity / tryptophan catabolic process to kynurenine
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
BENZOIC ACID PHENYLMETHYLESTER / : / DI(HYDROXYETHYL)ETHER / Putative cyclase
Similarity search - Component
Biological speciesLabrenzia aggregata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSommer, T. / Bjerregaard-Andersen, K. / Morth, J.P.
CitationJournal: Sci Rep / Year: 2018
Title: A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase.
Authors: Sommer, T. / Bjerregaard-Andersen, K. / Uribe, L. / Etzerodt, M. / Diezemann, G. / Gauss, J. / Cascella, M. / Morth, J.P.
History
DepositionApr 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: isatin hydrolase A
B: isatin hydrolase A
C: isatin hydrolase A
D: isatin hydrolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,86415
Polymers115,2414
Non-polymers1,62211
Water18,3931021
1
A: isatin hydrolase A
B: isatin hydrolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7099
Polymers57,6212
Non-polymers1,0887
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-62 kcal/mol
Surface area18540 Å2
MethodPISA
2
C: isatin hydrolase A
D: isatin hydrolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1556
Polymers57,6212
Non-polymers5344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-65 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.690, 70.670, 92.920
Angle α, β, γ (deg.)108.23, 95.94, 101.48
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
isatin hydrolase A


Mass: 28810.295 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The His-tag was visible in the density in this molecule
Source: (gene. exp.) Labrenzia aggregata (bacteria) / Gene: SIAM614_30646 / Production host: Escherichia coli (E. coli) / References: UniProt: A0P0F0

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Non-polymers , 6 types, 1032 molecules

#2: Chemical
ChemComp-BZM / BENZOIC ACID PHENYLMETHYLESTER


Mass: 212.244 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O2 / Comment: medication*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28 % PEG 1500 and 1 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.5→63.544 Å / Num. obs: 135214 / % possible obs: 95.7 % / Redundancy: 3 % / Net I/σ(I): 10
Reflection shellResolution: 1.5→1.54 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M8D

4m8d


Resolution: 1.5→63.544 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 16.66
RfactorNum. reflection% reflection
Rfree0.177 6635 4.91 %
Rwork0.1479 --
obs0.1493 135163 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→63.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 105 1021 9034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118432
X-RAY DIFFRACTIONf_angle_d1.09311536
X-RAY DIFFRACTIONf_dihedral_angle_d5.3377202
X-RAY DIFFRACTIONf_chiral_restr0.0731224
X-RAY DIFFRACTIONf_plane_restr0.0091534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.23482070.21294162X-RAY DIFFRACTION93
1.5171-1.53490.20542080.18774159X-RAY DIFFRACTION94
1.5349-1.55360.24171830.18554277X-RAY DIFFRACTION94
1.5536-1.57330.22932200.18174270X-RAY DIFFRACTION95
1.5733-1.5940.21462170.17424142X-RAY DIFFRACTION95
1.594-1.61590.20252420.17434181X-RAY DIFFRACTION95
1.6159-1.63890.21322520.16924275X-RAY DIFFRACTION95
1.6389-1.66340.19212020.16124182X-RAY DIFFRACTION95
1.6634-1.68940.18692220.15614262X-RAY DIFFRACTION95
1.6894-1.71710.18232500.1564243X-RAY DIFFRACTION95
1.7171-1.74670.20232460.15334198X-RAY DIFFRACTION95
1.7467-1.77850.20432440.15714224X-RAY DIFFRACTION96
1.7785-1.81270.20592210.15614295X-RAY DIFFRACTION96
1.8127-1.84970.18851980.15024310X-RAY DIFFRACTION96
1.8497-1.88990.20482230.15824308X-RAY DIFFRACTION96
1.8899-1.93390.19312290.15094241X-RAY DIFFRACTION96
1.9339-1.98220.16682350.14474339X-RAY DIFFRACTION96
1.9822-2.03580.18362030.14394274X-RAY DIFFRACTION97
2.0358-2.09570.16862530.14364322X-RAY DIFFRACTION97
2.0957-2.16340.1792550.14624254X-RAY DIFFRACTION97
2.1634-2.24070.18162110.14744314X-RAY DIFFRACTION97
2.2407-2.33040.17632260.15384325X-RAY DIFFRACTION97
2.3304-2.43650.1971850.14974387X-RAY DIFFRACTION97
2.4365-2.5650.18621900.15214376X-RAY DIFFRACTION98
2.565-2.72570.18292330.14924360X-RAY DIFFRACTION97
2.7257-2.93610.17532520.14764286X-RAY DIFFRACTION97
2.9361-3.23160.16042140.14734313X-RAY DIFFRACTION96
3.2316-3.69920.1512230.13434406X-RAY DIFFRACTION98
3.6992-4.66030.14412010.11834425X-RAY DIFFRACTION99
4.6603-63.60120.13821900.13814418X-RAY DIFFRACTION99

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