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- PDB-9fek: Crystal structure of guanidinase from Nitrospira inopinata -

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Basic information

Entry
Database: PDB / ID: 9fek
TitleCrystal structure of guanidinase from Nitrospira inopinata
ComponentsPutative agmatinase 2
KeywordsMETAL BINDING PROTEIN / comammox / guanidine / guanidinase / complete ammonia oxidizer
Function / homology
Function and homology information


agmatinase / agmatinase activity / metal ion binding
Similarity search - Function
Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / NICKEL (II) ION / Putative agmatinase 2
Similarity search - Component
Biological speciesCandidatus Nitrospira inopinata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPuehringer, D. / Mccarthy, A.
Funding support Austria, European Union, 4items
OrganizationGrant numberCountry
Vienna Science and Technology Fund (WWTF)FA705009 Austria
Christian Doppler ForschungsgesellschaftFA743017 Austria
University of Vienna Research Platform Comammox326300 Austria
European Regional Development FundFA263001European Union
CitationJournal: Nature / Year: 2024
Title: Growth of complete ammonia oxidizers on guanidine.
Authors: Palatinszky, M. / Herbold, C.W. / Sedlacek, C.J. / Puhringer, D. / Kitzinger, K. / Giguere, A.T. / Wasmund, K. / Nielsen, P.H. / Dueholm, M.K.D. / Jehmlich, N. / Gruseck, R. / Legin, A. / ...Authors: Palatinszky, M. / Herbold, C.W. / Sedlacek, C.J. / Puhringer, D. / Kitzinger, K. / Giguere, A.T. / Wasmund, K. / Nielsen, P.H. / Dueholm, M.K.D. / Jehmlich, N. / Gruseck, R. / Legin, A. / Kostan, J. / Krasnici, N. / Schreiner, C. / Palmetzhofer, J. / Hofmann, T. / Zumstein, M. / Djinovic-Carugo, K. / Daims, H. / Wagner, M.
History
DepositionMay 20, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionAug 14, 2024ID: 8C0H
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Aug 28, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 2, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative agmatinase 2
B: Putative agmatinase 2
C: Putative agmatinase 2
D: Putative agmatinase 2
E: Putative agmatinase 2
F: Putative agmatinase 2
G: Putative agmatinase 2
H: Putative agmatinase 2
I: Putative agmatinase 2
J: Putative agmatinase 2
K: Putative agmatinase 2
L: Putative agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)504,26760
Polymers500,59712
Non-polymers3,66948
Water50,7122815
1
A: Putative agmatinase 2
B: Putative agmatinase 2
C: Putative agmatinase 2
D: Putative agmatinase 2
E: Putative agmatinase 2
F: Putative agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,13330
Polymers250,2996
Non-polymers1,83524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44090 Å2
ΔGint-324 kcal/mol
Surface area57800 Å2
MethodPISA
2
G: Putative agmatinase 2
H: Putative agmatinase 2
I: Putative agmatinase 2
J: Putative agmatinase 2
K: Putative agmatinase 2
L: Putative agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,13330
Polymers250,2996
Non-polymers1,83524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44240 Å2
ΔGint-326 kcal/mol
Surface area58290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.965, 164.791, 143.965
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative agmatinase 2


Mass: 41716.457 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Nitrospira inopinata (bacteria)
Gene: speB, NITINOP_1173 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4KUT0, agmatinase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2815 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3547.55
22.3547.55
32.3547.55
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
295.151vapor diffusion, sitting drop5.60.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4
295.152vapor diffusion, sitting drop5.60.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4
295.153vapor diffusion, sitting drop5.60.5 M (NH4)2SO4, 0.1 M Na3 Citrate pH 5.6, 1 M Li2SO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
31003N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID30B10.9184
SYNCHROTRONESRF ID30B21.48253
SYNCHROTRONESRF ID30B31.89289
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELJun 4, 2022Vertical CRL / Horizontal Eliptical mirror
DECTRIS PILATUS 6M2PIXELDec 5, 2023Vertical CRL / Horizontal Eliptical mirror
DECTRIS PILATUS 6M3PIXELDec 5, 2023Vertical CRL / Horizontal Eliptical mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
3Si(111)SINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.482531
31.892891
Reflection

Entry-ID: 9FEK

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2CC starRmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.58-45.0158393692.892.322.070.9910.9980.10640.076730.131814.66
2.2-4858620595.863.623.370.9910.9980.1730.10650.203725.05
2.7-47.6229982895.263.630.30.9770.9940.24290.14870.285633.49
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allDiffraction-ID% possible all
1.58-1.6362.11.1910.56536860.2560.6390.90811.506185.24
2.2-2.233.71.081.07204320.4730.8010.65931.268294.66
2.7-2.733.60.92160.89103770.5880.860.56161.082394.07

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Processing

Software
NameVersionClassification
PHENIX(1.21_5184: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→45.01 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 2001 0.34 %
Rwork0.1998 --
obs0.1999 583176 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34269 0 144 2815 37228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00935364
X-RAY DIFFRACTIONf_angle_d1.09248095
X-RAY DIFFRACTIONf_dihedral_angle_d14.5212769
X-RAY DIFFRACTIONf_chiral_restr0.0655310
X-RAY DIFFRACTIONf_plane_restr0.0136341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.42321310.372737366X-RAY DIFFRACTION84
1.62-1.660.39021350.351240526X-RAY DIFFRACTION91
1.66-1.710.36821490.328942202X-RAY DIFFRACTION94
1.71-1.770.35321460.299342090X-RAY DIFFRACTION94
1.77-1.830.291440.280742203X-RAY DIFFRACTION95
1.83-1.90.26891410.249442424X-RAY DIFFRACTION95
1.9-1.990.26871510.222842652X-RAY DIFFRACTION96
1.99-2.10.21041530.203743029X-RAY DIFFRACTION96
2.1-2.230.19451440.186342663X-RAY DIFFRACTION96
2.23-2.40.21131490.17542147X-RAY DIFFRACTION94
2.4-2.640.1791420.171642398X-RAY DIFFRACTION95
2.64-3.020.17561390.176541571X-RAY DIFFRACTION93
3.02-3.810.17531460.175340800X-RAY DIFFRACTION91
3.81-45.010.19131310.178339104X-RAY DIFFRACTION87

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