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- PDB-7oi1: Crystal structure of Synechocystis sp PCC6803 guanidinium hydrolase -

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Basic information

Entry
Database: PDB / ID: 7oi1
TitleCrystal structure of Synechocystis sp PCC6803 guanidinium hydrolase
ComponentsProbable agmatinase 2
KeywordsMETAL BINDING PROTEIN / ureohydrolase family protein / arginase/agmatinase family protein / Ni2+ enzyme / 2-metal ion cluster
Function / homology
Function and homology information


agmatinase / putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / metal ion binding
Similarity search - Function
Agmatinase-related / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Probable agmatinase 2
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFleming, J.R. / Mayans, O.M.
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: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 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.title / _citation.year
Revision 1.2Mar 16, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Mar 23, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Mar 30, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Probable agmatinase 2
B: Probable agmatinase 2
C: Probable agmatinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,66420
Polymers129,4133
Non-polymers1,25017
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.360, 140.210, 86.850
Angle α, β, γ (deg.)90.000, 119.750, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-401-

CL

21A-545-

HOH

31B-526-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 11 through 249 or resid 251...
d_2ens_1(chain "B" and (resid 11 through 249 or resid 251...
d_3ens_1(chain "C" and (resid 11 through 249 or resid 251...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROVALA1 - 239
d_12ens_1VALCYSA241 - 277
d_13ens_1TRPTHRA279 - 319
d_14ens_1VALASPA321 - 378
d_21ens_1PROVALB1 - 239
d_22ens_1VALCYSB241 - 277
d_23ens_1TRPTHRB279 - 319
d_24ens_1VALASPB321 - 378
d_31ens_1PROVALC1 - 239
d_32ens_1VALCYSC241 - 277
d_33ens_1TRPTHRC279 - 319
d_34ens_1VALASPC321 - 378

NCS oper:
IDCodeMatrixVector
1given(-0.0937256241662, 0.675355028544, -0.731512879446), (0.672938974051, -0.498520911279, -0.546470528227), (-0.733736086463, -0.543481817946, -0.407748536459)3.56486623161, 36.1526151252, 37.6773356465
2given(-0.0926565806031, -0.672931680637, -0.733878539859), (-0.67226129145, -0.501416675025, 0.544652250546), (-0.734492691651, 0.543823750127, -0.405926366118)4.60117611622, -33.9536878922, 36.8382076606

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 43137.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: speB2, sll1077 / Production host: Escherichia coli (E. coli) / References: UniProt: P73270, agmatinase

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Non-polymers , 6 types, 415 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Ni
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1mM sodium citrate pH 5.5, 40% [v/v] PEG 600

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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: 1.9→29.15 Å / Num. obs: 82121 / % possible obs: 97.8 % / Redundancy: 7 % / Biso Wilson estimate: 38.66 Å2 / CC1/2: 0.998 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.92 Å / Num. unique obs: 2561 / CC1/2: 0.548

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Processing

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

3nio


Resolution: 1.9→29.15 Å / SU ML: 0.2751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 2453 2.99 %
Rwork0.1728 79497 -
obs0.1739 81950 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8748 0 50 398 9196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00759009
X-RAY DIFFRACTIONf_angle_d0.906412251
X-RAY DIFFRACTIONf_chiral_restr0.05661372
X-RAY DIFFRACTIONf_plane_restr0.00911605
X-RAY DIFFRACTIONf_dihedral_angle_d13.5473303
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.21296469663
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.219836565096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.48951300.43924221X-RAY DIFFRACTION93.55
1.93-1.970.44991320.37174393X-RAY DIFFRACTION97.46
1.97-2.020.37351390.32344408X-RAY DIFFRACTION97.85
2.02-2.060.31361400.2844390X-RAY DIFFRACTION97.71
2.06-2.110.28821300.25054417X-RAY DIFFRACTION97.76
2.11-2.170.27151310.22724413X-RAY DIFFRACTION97.99
2.17-2.230.29981380.21944435X-RAY DIFFRACTION98.26
2.23-2.310.29321390.21554403X-RAY DIFFRACTION98.16
2.31-2.390.24481340.19074420X-RAY DIFFRACTION97.91
2.39-2.480.24921410.18634457X-RAY DIFFRACTION98.21
2.48-2.60.29831340.18694390X-RAY DIFFRACTION97.25
2.6-2.730.22111360.17554304X-RAY DIFFRACTION95.55
2.73-2.910.19481430.17494485X-RAY DIFFRACTION98.83
2.91-3.130.23191390.16484449X-RAY DIFFRACTION98.99
3.13-3.440.1851420.16164511X-RAY DIFFRACTION99.17
3.44-3.940.15831340.14574467X-RAY DIFFRACTION98.67
3.94-4.960.16561310.13454418X-RAY DIFFRACTION97.14
4.96-29.150.16731400.15344516X-RAY DIFFRACTION98.17
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7834406256340.01421653616120.06375074954680.822767696849-0.1579570249130.556491949527-0.0108400425420.02727242188610.0213038173410.01489977174050.00574427321489-0.212434402219-0.02921319985610.1903663496770.009611473711790.342034384065-0.01354828306680.002702940258340.449496148381-0.009233477980320.4535601780926.210485064273.0670116578836.9159685667
21.13515083833-0.0331619456977-0.1623410512710.5493886280610.148704916340.8482715234530.0005403064805990.2322728526350.193790816374-0.140658656813-0.006301075365840.0157720343787-0.215856283411-0.03324537165010.005740693372420.4200561357940.00249029286466-0.009384008447640.398883390950.0740044971890.37966398515-21.942232990818.605490384516.4397027508
30.9807796626450.204768532714-0.03012456904430.712437194467-0.2104457577540.820665350642-0.02381022682650.26165768812-0.255506713855-0.1447441640950.0460229738093-0.01352719615430.136699915138-0.00630429599902-0.01565955704840.405013383475-0.00678065591765-0.01768953520490.385372421127-0.0829145576820.41892727434-25.1171576351-19.53378450118.9958569188
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 11 - 388 / Label seq-ID: 1 - 378

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 11 through 388)AA
22(chain 'B' and resid 11 through 388)BB
33(chain 'C' and resid 11 through 388)CC

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