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- PDB-7esr: Crystal structure of Synechocystis sp PCC6803 guanidinium hydrola... -

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Basic information

Entry
Database: PDB / ID: 7esr
TitleCrystal structure of Synechocystis sp PCC6803 guanidinium hydrolase (R32)
ComponentsProbable agmatinase 2
KeywordsHYDROLASE / ureohydrolase family protein / arginase/agmatinase family protein / Ni2+ enzyme / 2-metal ion cluster / METAL BINDING PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / putrescine biosynthetic process from arginine, via agmatine / agmatinase activity / metal ion binding / cytoplasm
Similarity search - Function
Agmatinase-related / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Guanidine hydrolase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMayans, O.M. / Fleming, J.R.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council (ERC)681777 Germany
CitationJournal: Nature / Year: 2022
Title: Discovery of a Ni 2+ -dependent guanidine hydrolase in bacteria.
Authors: Funck, D. / Sinn, M. / Fleming, J.R. / Stanoppi, M. / Dietrich, J. / Lopez-Igual, R. / Mayans, O. / Hartig, J.S.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: 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.year
Revision 1.2Mar 23, 2022Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4016
Polymers43,1381
Non-polymers2635
Water5,855325
1
A: Probable agmatinase 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)260,40736
Polymers258,8276
Non-polymers1,58030
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area46110 Å2
ΔGint-332 kcal/mol
Surface area56440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.700, 140.700, 95.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-623-

HOH

31A-657-

HOH

41A-709-

HOH

51A-922-

HOH

61A-923-

HOH

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Components

#1: Protein Probable agmatinase 2 / guanidine hydrolase / Agmatine ureohydrolase 2 / AUH 2


Mass: 43137.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P73270, agmatinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.06 M (0.3M magnesium chloride hexahydrate, 0.3M calcium chloride dehydrate), 0.1M (1M HEPES; MOPS) pH7.5, 30 % [v/v] (40% [v/v] ethylene glycol, 20% [w/v] PEG 8000)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→28.97 Å / Num. obs: 67577 / % possible obs: 99.03 % / Redundancy: 9.4 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.24
Reflection shellResolution: 1.42→1.43 Å / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1320 / CC1/2: 0.515

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NIO

3nio


Resolution: 1.42→28.97 Å / SU ML: 0.2038 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.4013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1476 2026 3 %
Rwork0.1317 65502 -
obs0.1322 67528 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.42→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2917 0 14 325 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00783022
X-RAY DIFFRACTIONf_angle_d1.00744114
X-RAY DIFFRACTIONf_chiral_restr0.0838462
X-RAY DIFFRACTIONf_plane_restr0.0125540
X-RAY DIFFRACTIONf_dihedral_angle_d13.78781117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.450.53851310.56764289X-RAY DIFFRACTION91.15
1.45-1.490.37291350.38324537X-RAY DIFFRACTION96.97
1.49-1.540.27371540.23834654X-RAY DIFFRACTION99.75
1.54-1.590.20721460.18254727X-RAY DIFFRACTION99.86
1.59-1.640.18261410.16774676X-RAY DIFFRACTION99.92
1.64-1.710.17111300.15534721X-RAY DIFFRACTION99.94
1.71-1.790.16261390.144687X-RAY DIFFRACTION99.96
1.79-1.880.15331550.12164703X-RAY DIFFRACTION99.67
1.88-20.13061630.10964689X-RAY DIFFRACTION99.9
2-2.150.13541550.10564726X-RAY DIFFRACTION99.94
2.15-2.370.10841410.10384711X-RAY DIFFRACTION100
2.37-2.710.11931570.114738X-RAY DIFFRACTION99.71
2.71-3.420.13111230.11274776X-RAY DIFFRACTION99.98
3.42-28.970.14721560.13254868X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: -2.38772611308 Å / Origin y: 22.083574978 Å / Origin z: 16.9110270252 Å
111213212223313233
T0.258729180738 Å20.00843531641217 Å20.0193171545241 Å2-0.194165299095 Å2-0.0293811805589 Å2--0.224638873946 Å2
L0.339457954139 °2-0.0562730271783 °20.0878028838993 °2-0.211379301423 °2-0.0171939612654 °2--0.501229659144 °2
S0.00407398972877 Å °-0.0717736016072 Å °0.103407023063 Å °0.0715845361783 Å °0.0183402010039 Å °-0.0044967133708 Å °-0.173456396425 Å °-0.0197531095409 Å °-1.71003487009E-6 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 11 through 601)

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