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- PDB-6hrg: Structure of Igni18, a novel metallo hydrolase from the hyperther... -

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Basic information

Entry
Database: PDB / ID: 6hrg
TitleStructure of Igni18, a novel metallo hydrolase from the hyperthermophilic archaeon Ignicoccus hospitalis KIN4/I
ComponentsUPF0173 metal-dependent hydrolase Igni_1254
KeywordsHYDROLASE / Ignococcus hospitalis / metallo-B-lactamase
Function / homology
Function and homology information


Protein of unknown funcion UPF0173 / Beta-lactamase superfamily domain / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / UPF0173 metal-dependent hydrolase Igni_1254
Similarity search - Component
Biological speciesIgnicoccus hospitalis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsSmits, S.H. / Streit, W.R. / Jaeger, K.E. / Hoeppner, A.
CitationJournal: Commun Biol / Year: 2021
Title: A promiscuous ancestral enzyme ́s structure unveils protein variable regions of the highly diverse metallo-beta-lactamase family.
Authors: Perez-Garcia, P. / Kobus, S. / Gertzen, C.G.W. / Hoeppner, A. / Holzscheck, N. / Strunk, C.H. / Huber, H. / Jaeger, K.E. / Gohlke, H. / Kovacic, F. / Smits, S.H.J. / Streit, W.R. / Chow, J.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UPF0173 metal-dependent hydrolase Igni_1254
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9735
Polymers28,7081
Non-polymers2654
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-80 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.420, 67.420, 253.770
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-303-

PO4

21A-303-

PO4

31A-469-

HOH

41A-488-

HOH

51A-493-

HOH

61A-494-

HOH

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Components

#1: Protein UPF0173 metal-dependent hydrolase Igni_1254


Mass: 28707.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignicoccus hospitalis (archaea) / Gene: Igni_1254 / Production host: Komagataella pastoris (fungus) / References: UniProt: A8ABX8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 273 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8 and 22 % (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.12→84.59 Å / Num. obs: 12063 / % possible obs: 99.87 % / Redundancy: 6.8 % / Net I/σ(I): 12.6
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→84.59 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.093 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.263 / ESU R Free: 0.215
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 989 7.6 %RANDOM
Rwork0.1843 ---
obs0.1891 12063 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.47 Å2 / Biso mean: 37.05 Å2 / Biso min: 16.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.12→84.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 8 97 1898
Biso mean--45.29 38.63 -
Num. residues----233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191855
X-RAY DIFFRACTIONr_bond_other_d0.0010.021743
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9662525
X-RAY DIFFRACTIONr_angle_other_deg0.80734049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00924.475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95715302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.94155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 2.119→2.174 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 68 -
Rwork0.236 887 -
all-955 -
obs--100 %

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