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- PDB-8d27: Arginase Domain of Ornithine Decarboxylase/Arginase from Fusobact... -

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Basic information

Entry
Database: PDB / ID: 8d27
TitleArginase Domain of Ornithine Decarboxylase/Arginase from Fusobacterium nucleatum
ComponentsArginase
KeywordsHYDROLASE / arginase domain / ornithine decarboxylase/arginase / inactive / ODA
Function / homology
Function and homology information


arginine metabolic process / arginase activity / lyase activity / metal ion binding
Similarity search - Function
Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Arginase / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily ...Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Arginase / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Biological speciesFusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsChan, A.C. / Kolesnikov, M. / Murphy, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2022
Title: Sequence Divergence in the Arginase Domain of Ornithine Decarboxylase/Arginase in Fusobacteriacea Leads to Loss of Function in Oral Associated Species.
Authors: Mothersole, R.G. / Kolesnikov, M. / Chan, A.C.K. / Oduro, E. / Murphy, M.E.P. / Wolthers, K.R.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase
B: Arginase


Theoretical massNumber of molelcules
Total (without water)64,1632
Polymers64,1632
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.818, 78.217, 73.530
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginase


Mass: 32081.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. nucleatum ATCC 25586 (bacteria)
Strain: ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355
Gene: FN0501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q8RG18
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 1.24 ° / Mosaicity esd: 0.012 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.07 M sodium acetate pH 4.6, 12% PEG 4000 and 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.45
ReflectionResolution: 2.25→50 Å / Num. obs: 23357 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.089 / Rrim(I) all: 0.171 / Χ2: 1.055 / Net I/σ(I): 6 / Num. measured all: 81549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.292.90.4889980.6630.3230.5870.77683.8
2.29-2.3330.4410500.7310.2880.5280.75988.1
2.33-2.3830.46111010.7530.3030.5530.82292.1
2.38-2.423.20.45911200.7160.2980.5490.77494.7
2.42-2.483.30.42711650.7480.2740.5080.84497.1
2.48-2.533.40.411740.8070.2490.4720.87898.7
2.53-2.63.50.37711780.840.2320.4430.8999.7
2.6-2.673.60.3811780.8510.2310.4460.9299.2
2.67-2.753.60.31211920.8840.190.3660.89699.4
2.75-2.833.60.29311890.9130.1770.3430.99599.3
2.83-2.943.60.26311900.9150.1590.3081.09499.7
2.94-3.053.60.2112030.930.1270.2461.07699.6
3.05-3.193.60.17911980.9510.1080.211.2799.6
3.19-3.363.60.15611700.9560.0940.1821.3499.7
3.36-3.573.60.1312040.9640.0790.1521.25799.3
3.57-3.853.70.11711860.9660.070.1361.30799.4
3.85-4.233.80.10511930.9760.0630.1231.3499.6
4.23-4.853.80.08912200.9750.0530.1041.222100
4.85-6.13.80.08912250.9780.0530.1041.091100
6.1-503.70.07512230.9880.0450.0871.10999

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.5
Highest resolutionLowest resolution
Rotation44.82 Å2.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 2.25→44.82 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2123 1072 4.59 %
Rwork0.1805 22284 -
obs0.1944 23341 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.02 Å2 / Biso mean: 34.9491 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 2.25→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 77 4447
Biso mean---28.74 -
Num. residues----562
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.360.25431230.25142372249580
2.36-2.480.28911650.24112683284889
2.48-2.640.25121390.242838297794
2.64-2.840.26771370.22342827296495
2.84-3.130.25241540.21262833298795
3.13-3.580.2274960.19112895299196
3.58-4.510.19111140.16232919303396
4.51-44.820.18711290.16292917304695
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)
1-0.00020.0002-0.00040.0027-0.0040.00550.00560.00680.0002-0.016-0.00350.0010.0106-0.0055-0.00960.15210.00830.00160.34350.01520.070120.09733.890655.8443
20.0016-0.0009-0.0030.00380.00450.008-0.008-0.0012-0.00240.0025-0.00340.00520.0297-0.0193-0.04650.14660.01070.01290.3809-0.02150.084416.43937.868967.7651
3-0.00020.00020.00010.00080.00010.00020.003-0.00820.00020.00470.00490.0003-0.0246-0.00540.01670.22490.00480.00340.3922-0.01860.089617.355845.544775.3159
40.01410.0043-0.00360.0013-0.00070.0055-0.00410.0111-0.00070.0038-0.01290.0027-0.00130.0037-0.03480.2026-0.0160.01180.3327-0.0120.080128.715542.177678.4597
50.00520.00350.00480.0050.00360.00940.01320.00320.00060.0108-0.0001-0.0023-0.00210.00690.01630.2431-0.04550.00610.3868-0.00670.095733.088547.861168.0684
60.0009-0.0002-0.003300.00060.0121-0.0010.01520.0028-0.02210.0078-0.0012-0.0169-0.00490.00530.2389-0.00070.0060.32980.00830.074333.116440.090761.8854
70.0037-0.0034-0.00250.00520.0010.0044-0.0010.0041-0.00240.0083-0.00610.0014-0.00040.001-0.01020.255-0.00580.01150.37140.0140.093812.687639.967137.6576
80.0085-0.00190.00370.0004-0.00080.0017-0.0106-0.00180.00040.0016-0.0001-0.0031-0.00170.0104-0.02040.24290.0158-0.00850.31760.00870.07534.104434.317439.5606
90.0020.00110.00440.00060.00250.0102-0.0042-0.01260.00170.02660.0014-0.0036-0.00590.0045-0.01450.23160.015-0.01180.35340.00260.082423.950638.263234.7981
100.00060.00050.00140.0006-0.00010.007-0.00130.00020.0002-0.0016-0.00110.00120.0078-0.0036-0.00290.20490.01190.00210.3087-0.01250.074412.389538.818827.002
110.00310.0002-0.00080.00140.00250.0058-0.0103-0.0041-0.00190.0003-0.0091-0-0.0057-0.0076-0.04380.2072-0.0230.0010.29880.00540.067120.757550.178828.4682
120.01060.00330.00780.00520.00520.00740.00020.00110.0034-0.01190.01420.0048-0.0072-0.0250.00370.26920.02240.01760.39360.00210.097418.64848.007220.722
130.00080.00150.00140.00270.00270.00270.010.02080.00340.0068-0.00380.003-0.0093-0.0106-0.00010.2509-0.00410.02780.39030.01330.09379.204358.103223.8429
140.0370.0006-0.01230.002-0.00340.01-0.01160.0249-0.0094-0.01020.00240.00210.0019-0.0055-0.00170.2399-0.0199-0.00770.38430.01110.09350.118253.037531.6156
150.0062-0.0038-0.00050.0030.00180.0038-0.0125-0.010.00260.01070.0137-0.0033-0.00940.00860.01270.26460.0074-0.01370.35930.01190.08671.506643.643233.7887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 501 through 576 )A501 - 576
2X-RAY DIFFRACTION2chain 'A' and (resid 577 through 642 )A577 - 642
3X-RAY DIFFRACTION3chain 'A' and (resid 643 through 687 )A643 - 687
4X-RAY DIFFRACTION4chain 'A' and (resid 688 through 714 )A688 - 714
5X-RAY DIFFRACTION5chain 'A' and (resid 715 through 746 )A715 - 746
6X-RAY DIFFRACTION6chain 'A' and (resid 747 through 781 )A747 - 781
7X-RAY DIFFRACTION7chain 'B' and (resid 501 through 517 )B501 - 517
8X-RAY DIFFRACTION8chain 'B' and (resid 518 through 539 )B518 - 539
9X-RAY DIFFRACTION9chain 'B' and (resid 540 through 575 )B540 - 575
10X-RAY DIFFRACTION10chain 'B' and (resid 576 through 598 )B576 - 598
11X-RAY DIFFRACTION11chain 'B' and (resid 599 through 642 )B599 - 642
12X-RAY DIFFRACTION12chain 'B' and (resid 643 through 661 )B643 - 661
13X-RAY DIFFRACTION13chain 'B' and (resid 662 through 714 )B662 - 714
14X-RAY DIFFRACTION14chain 'B' and (resid 715 through 746 )B715 - 746
15X-RAY DIFFRACTION15chain 'B' and (resid 747 through 781 )B747 - 781

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