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- PDB-8x3g: Crystal structure of metformin hydrolase from Aminobacter -

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Basic information

Entry
Database: PDB / ID: 8x3g
TitleCrystal structure of metformin hydrolase from Aminobacter
Components
  • Agmatinase family protein
  • Arginase family protein
KeywordsHYDROLASE / Metformin hydrolase / arginase family / heterohexamer
Function / homology: / : / :
Function and homology information
Biological speciesAminobacter sp. NyZ550 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLi, T. / Zhou, N.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32230001 China
CitationJournal: Nat Commun / Year: 2024
Title: Discovery of a Ni 2+ -dependent heterohexameric metformin hydrolase.
Authors: Li, T. / Xu, Z.J. / Zhang, S.T. / Xu, J. / Pan, P. / Zhou, N.Y.
History
DepositionNov 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agmatinase family protein
B: Agmatinase family protein
C: Arginase family protein
D: Arginase family protein
E: Arginase family protein
F: Arginase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,95112
Polymers236,5476
Non-polymers4046
Water28,3921576
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26970 Å2
ΔGint-154 kcal/mol
Surface area56830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.430, 152.522, 173.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Agmatinase family protein / Metformin hydrolase alpha subunit


Mass: 42224.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A metformin degrader / Source: (gene. exp.) Aminobacter sp. NyZ550 (bacteria) / Strain: NyZ550 / Gene: N7E70_023840 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A9E9PQ69
#2: Protein
Arginase family protein


Mass: 38024.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A metformin degrader / Source: (gene. exp.) Aminobacter sp. NyZ550 (bacteria) / Strain: NYZ550 / Gene: N7E70_023835 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A9E9PPA5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1576 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.15 M calcium chloride dihydrate, 0.1 M MES buffer system (pH 6.2), 5% (v/v) glycerol, 15% (v/v) PEG smear broad

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.84→39.47 Å / Num. obs: 205966 / % possible obs: 99.95 % / Redundancy: 10 % / CC1/2: 0.995 / Net I/σ(I): 12.7
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 10015 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→39.47 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.182 10299 5 %
Rwork0.1525 --
obs0.154 205966 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15355 0 16 1576 16947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01815713
X-RAY DIFFRACTIONf_angle_d1.47921272
X-RAY DIFFRACTIONf_dihedral_angle_d14.3425792
X-RAY DIFFRACTIONf_chiral_restr0.1082287
X-RAY DIFFRACTIONf_plane_restr0.0192808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.2693370.22376412X-RAY DIFFRACTION99
1.87-1.890.25943400.20566457X-RAY DIFFRACTION100
1.89-1.910.23133380.18736430X-RAY DIFFRACTION100
1.91-1.930.22873400.17516462X-RAY DIFFRACTION100
1.93-1.960.20473420.15986486X-RAY DIFFRACTION100
1.96-1.990.20053400.15926456X-RAY DIFFRACTION100
1.99-2.020.19343420.15866500X-RAY DIFFRACTION100
2.02-2.050.19293380.15946427X-RAY DIFFRACTION100
2.05-2.080.19693410.15336472X-RAY DIFFRACTION100
2.08-2.110.21583430.15736514X-RAY DIFFRACTION100
2.11-2.150.19383400.16116475X-RAY DIFFRACTION100
2.15-2.190.19443400.15086454X-RAY DIFFRACTION100
2.19-2.230.19273410.15476484X-RAY DIFFRACTION100
2.23-2.270.19133440.15476532X-RAY DIFFRACTION100
2.27-2.320.18643400.15736462X-RAY DIFFRACTION100
2.32-2.380.18953420.15576500X-RAY DIFFRACTION100
2.38-2.440.18143430.15986513X-RAY DIFFRACTION100
2.44-2.50.20133420.15276493X-RAY DIFFRACTION100
2.5-2.580.19653430.15636525X-RAY DIFFRACTION100
2.58-2.660.17853440.15576534X-RAY DIFFRACTION100
2.66-2.760.19553420.1546498X-RAY DIFFRACTION100
2.76-2.870.18783430.15776507X-RAY DIFFRACTION100
2.87-30.17853460.15516572X-RAY DIFFRACTION100
3-3.150.18983440.1556545X-RAY DIFFRACTION100
3.15-3.350.18553460.15626576X-RAY DIFFRACTION100
3.35-3.610.15343450.1426556X-RAY DIFFRACTION100
3.61-3.970.15823470.13256589X-RAY DIFFRACTION100
3.97-4.550.13313490.12216636X-RAY DIFFRACTION100
4.55-5.730.17353520.14256684X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.95181.52611.06598.67774.55796.75410.1221-0.34990.06130.7532-0.22370.4840.10960.00810.11090.2203-0.01710.0390.17920.0180.1292-0.2385-25.8551-26.5217
25.76391.66360.49272.62153.20164.43620.0042-0.3351-0.03810.321-0.0271-0.18580.2381-0.05370.0220.14910.0206-0.03580.09830.00630.11647.1522-29.4137-33.2894
30.7062-0.32170.37431.938-0.60141.32230.0249-0.1237-0.00270.2420.0237-0.02370.03380.0108-0.04740.1192-0.005-0.00750.1148-0.02210.0945.8785-10.6903-34.3339
41.44740.5998-0.70142.835-1.93636.76550.048-0.15920.07060.21360.01870.1476-0.2155-0.1028-0.05030.1027-0.00680.00310.0918-0.03880.11712.90191.1384-34.937
54.1966-2.1205-4.83734.57575.0028.7135-0.005-0.07350.14530.17460.02460.09390.0840.039-0.01130.11950.0032-0.01740.06360.02310.099411.06237.1359-31.1582
61.8955-0.6782-0.12.13330.25312.2240.0142-0.05840.10490.07340.0592-0.1913-0.09840.1744-0.06680.1027-0.0145-0.00040.0938-0.01810.116720.79599.9345-42.4988
71.0703-0.4315-0.25442.77031.88993.16680.0479-0.0532-0.03940.13880.0715-0.18730.05810.1961-0.12620.10230.0098-0.01660.10520.01150.129521.0203-4.1962-39.2009
83.24480.83462.84183.85753.14149.42470.0332-0.31280.04070.5333-0.0673-0.11460.2553-0.0340.03060.15670.0154-0.0330.09850.00080.142118.3829-12.1376-29.2724
93.61581.4725-0.29034.945-1.3193.03830.073-0.28480.04480.3921-0.0770.26870.0215-0.14830.00670.12610.01280.01660.1382-0.0180.0985-12.712-8.8163-39.7292
101.0237-0.4989-0.01951.7952-0.02520.5397-0.0192-0.1191-0.050.23950.03330.0980.0408-0.0591-0.01760.1216-0.01130.00260.12160.00480.0785-9.6006-28.8944-43.1134
114.86543.4332-5.40964.5508-2.1367.49510.0707-0.05920.03530.330.06360.07340.0605-0.1607-0.11490.12510.02220.00440.08670.02420.1236-15.5262-43.644-46.7311
121.8802-0.25090.1031.4112-0.25451.4558-0.04050.0449-0.0744-0.01540.04340.04260.1011-0.0493-0.00410.104-0.00650.00820.0748-0.00450.0833-9.905-46.7026-60.4401
135.67522.4172-2.7782.2717-1.76283.1414-0.09430.2227-0.0451-0.08730.07960.10.0505-0.11380.01020.11450.03040.0040.0607-0.01830.1001-13.8997-35.4527-60.7725
144.02442.4821-2.23814.2648-2.1372.36680.0476-0.0528-0.0094-0.0135-0.0480.03350.017-0.0729-0.01660.11660.03540.00410.0684-0.05620.04-11.216-28.4466-57.2535
155.68043.4-3.77154.9434-0.93673.46890.10810.06240.22980.1377-0.04050.40660.0129-0.2447-0.05320.12270.0121-0.02360.12610.01460.1016-20.3123-24.3915-52.5513
164.90521.2726-5.36931.2909-0.45237.21120.038-0.05950.20.0652-0.1557-0.69810.05960.63690.0890.17070.07250.02430.25510.06620.399111.4188-49.7576-67.4644
173.5094-0.6794-0.2817.27850.32353.8118-0.0815-0.06350.0548-0.3497-0.2307-0.7498-0.13730.21070.25350.12330.00280.04450.25580.02860.230816.0467-35.9485-78.6308
181.33910.4757-0.80781.5901-0.46191.4377-0.10760.2293-0.0037-0.38370.1009-0.1882-0.01350.0412-0.00340.2159-0.05110.04410.2077-0.02610.13626.6862-31.2179-89.3227
193.77233.74883.61026.9396.32919.8468-0.16330.01930.0863-0.18540.3153-0.3145-0.34560.3257-0.16750.08770.03090.01230.13690.0240.17479.285-30.1593-78.6079
200.68442.03-1.1186.9324-2.61173.9215-0.17970.1144-0.1161-0.49770.0786-0.25780.2319-0.01510.11710.02140.0330.02290.1665-0.00360.1362-0.1169-48.3284-74.3946
210.92780.1833-0.30491.10670.31293.7679-0.06760.20990.085-0.27910.0142-0.1503-0.24520.25830.04870.1795-0.00480.01330.18890.05110.18073.06421.335-75.6369
225.8982-2.98097.24823.278-5.41162.018-0.1959-0.04580.4904-0.00310.1867-0.0588-0.845-0.15910.05380.25-0.0023-0.02660.1320.03350.2477-3.927814.3279-67.2518
230.55590.1445-0.06421.2430.12331.0567-0.03820.07950.1801-0.1528-0.00110.286-0.1734-0.21150.02850.13490.0423-0.0410.16630.02280.1957-17.5226-0.3795-66.471
241.8066-0.29460.9462.7092-1.27174.1503-0.02770.2820.0163-0.3515-0.00350.00350.00920.0620.04140.12770.00620.01480.13910.00340.1159-6.9751-9.0217-75.5843
254.932-1.3025-5.29872.50982.49697.03320.36970.7044-0.0122-0.5245-0.31340.2475-0.0376-0.4211-0.0470.30220.1007-0.0430.27070.05750.222117.427912.7162-64.8636
265.47782.2169-0.51918.57830.06994.63190.1920.2115-0.287-0.737-0.2119-0.0108-0.0047-0.21610.00650.21690.09620.01820.3187-0.01240.141527.8003-1.2539-76.7538
271.1019-0.1371.14456.92325.58536.77020.1126-0.00660.0881-0.2633-0.27720.2858-0.2673-0.42280.16910.16250.0690.04160.21630.01330.158624.2546.181-61.6545
285.46920.93710.59456.19561.96183.81530.03230.6642-0.3185-0.7941-0.01870.1908-0.2164-0.276-0.01420.32730.0901-0.00660.30960.00110.174829.5741-0.2972-84.559
292.0504-1.7997-0.38714.3616-0.78343.73870.16960.19910.0567-0.3072-0.1817-0.0465-0.1359-0.02010.02040.13830.00930.02930.2056-0.03780.15440.1724-5.3015-76.455
301.1812-0.092-0.31731.96340.17853.25350.01520.0772-0.0879-0.09290.0092-0.3450.13340.3331-0.02890.11760.02710.02350.2101-0.04270.246645.3004-11.3617-68.6928
310.913-1.139-0.57664.02061.29121.23970.0170.06550.0022-0.1510.0302-0.1951-0.03470.0647-0.04070.11480.00770.00460.1782-0.01380.120731.1412-0.0509-59.7876
326.3587-2.568-0.36956.6328-2.59717.44690.27160.5565-0.3171-0.8327-0.2795-0.33570.54130.1311-0.00330.23220.0480.04250.2599-0.10290.306930.4549-45.4815-64.769
338.1917-1.0721-7.36420.89081.86047.6752-0.03390.3526-0.286-0.1228-0.0042-0.0431-0.0047-0.25710.01640.15980.0339-0.0510.1235-0.04160.196421.6662-35.9995-56.2841
344.08244.6471-1.28125.3135-1.5760.6466-0.1510.1064-0.2943-0.30720.0896-0.45840.09330.10690.06520.1820.06290.02230.2286-0.02830.263432.6302-36.3463-61.0155
352.0208-6.4282-2.64374.52580.98772.9199-0.4507-0.2066-0.82570.12130.1797-0.03280.57030.16410.21540.22890.0433-0.04450.1676-0.04380.389623.297-51.316-49.8349
361.09850.0078-0.37051.02980.13840.59120.0239-0.1862-0.19840.25530.0032-0.39660.15350.2086-0.0160.2160.068-0.10020.21660.01630.289229.1637-36.3864-37.6673
372.124-2.0787-0.37264.79-0.55991.9412-0.0317-0.11410.41860.0060.0592-0.76750.00620.2507-0.02670.14220.0129-0.02580.1595-0.04080.212432.2715-23.864-47.159
387.0492-3.6229-0.4053.8525-0.08311.48050.12470.2614-0.0332-0.1617-0.1152-0.39620.0020.1733-0.0120.13550.0168-0.0130.1392-0.04740.18229.8015-30.3788-53.9625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 129 )
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 252 )
7X-RAY DIFFRACTION7chain 'A' and (resid 253 through 329 )
8X-RAY DIFFRACTION8chain 'A' and (resid 330 through 357 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 46 )
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 182 )
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 252 )
13X-RAY DIFFRACTION13chain 'B' and (resid 253 through 297 )
14X-RAY DIFFRACTION14chain 'B' and (resid 298 through 329 )
15X-RAY DIFFRACTION15chain 'B' and (resid 330 through 357 )
16X-RAY DIFFRACTION16chain 'C' and (resid 6 through 39 )
17X-RAY DIFFRACTION17chain 'C' and (resid 40 through 80 )
18X-RAY DIFFRACTION18chain 'C' and (resid 81 through 291 )
19X-RAY DIFFRACTION19chain 'C' and (resid 292 through 310 )
20X-RAY DIFFRACTION20chain 'C' and (resid 311 through 345 )
21X-RAY DIFFRACTION21chain 'D' and (resid 25 through 108 )
22X-RAY DIFFRACTION22chain 'D' and (resid 109 through 126 )
23X-RAY DIFFRACTION23chain 'D' and (resid 127 through 259 )
24X-RAY DIFFRACTION24chain 'D' and (resid 260 through 335 )
25X-RAY DIFFRACTION25chain 'E' and (resid 6 through 39 )
26X-RAY DIFFRACTION26chain 'E' and (resid 40 through 69 )
27X-RAY DIFFRACTION27chain 'E' and (resid 70 through 95 )
28X-RAY DIFFRACTION28chain 'E' and (resid 96 through 126 )
29X-RAY DIFFRACTION29chain 'E' and (resid 127 through 172 )
30X-RAY DIFFRACTION30chain 'E' and (resid 173 through 259 )
31X-RAY DIFFRACTION31chain 'E' and (resid 260 through 344 )
32X-RAY DIFFRACTION32chain 'F' and (resid 25 through 46 )
33X-RAY DIFFRACTION33chain 'F' and (resid 47 through 80 )
34X-RAY DIFFRACTION34chain 'F' and (resid 81 through 108 )
35X-RAY DIFFRACTION35chain 'F' and (resid 109 through 126 )
36X-RAY DIFFRACTION36chain 'F' and (resid 127 through 259 )
37X-RAY DIFFRACTION37chain 'F' and (resid 260 through 291 )
38X-RAY DIFFRACTION38chain 'F' and (resid 292 through 329 )

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