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- PDB-7nnw: Crystal structure of Mycobacterium tuberculosis ArgF in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nnw
TitleCrystal structure of Mycobacterium tuberculosis ArgF in complex with methyl 4-hydroxy-3-iodobenzoate.
ComponentsOrnithine carbamoyltransferase
KeywordsTRANSFERASE / ArgF / Ornithine Carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / arginine biosynthetic process via ornithine / citrulline biosynthetic process / arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function
Ornithine carbamoyltransferase / Ornithine/putrescine carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
Similarity search - Domain/homology
methyl 3-iodanyl-4-oxidanyl-benzoate / PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsMendes, V. / Gupta, P. / Burgess, A. / Sebastian-Perez, V. / Cattermole, E. / Meghir, C. / Blundell, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1158806 United States
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / ...Authors: Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / Blundell, T.L. / Tiwari, S. / Mendes, V.
History
DepositionFeb 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,48818
Polymers199,2506
Non-polymers2,23812
Water24,7711375
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,83910
Polymers99,6253
Non-polymers1,2147
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-45 kcal/mol
Surface area31160 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6498
Polymers99,6253
Non-polymers1,0245
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-33 kcal/mol
Surface area30760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.802, 143.512, 97.524
Angle α, β, γ (deg.)90.000, 117.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ornithine carbamoyltransferase / OTCase


Mass: 33208.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argF, Rv1656, MTCY06H11.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WIT9, ornithine carbamoyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-98T / methyl 3-iodanyl-4-oxidanyl-benzoate


Mass: 278.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H7IO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1375 / 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: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 150 mM ammonium dihydrogen phosphate 10 mM praseodymium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→86.36 Å / Num. obs: 423088 / % possible obs: 99.9 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.04 / Rrim(I) all: 0.094 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.875.31.284166972313020.530.6121.4261.1100
5.62-86.3650.0383430868980.9980.0180.04234.299.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.05 Å86.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.1data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P2G
Resolution: 1.78→53.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 20506 4.85 %
Rwork0.1814 402582 -
obs0.1826 423088 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 35.3535 Å2 / Biso min: 17.75 Å2
Refinement stepCycle: final / Resolution: 1.78→53.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13502 0 102 1376 14980
Biso mean--52.66 42.9 -
Num. residues----1805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.80.39437400.3755133151405599
1.8-1.820.36197210.35241340414125100
1.82-1.840.34517030.33791350414207100
1.84-1.860.32726770.31381334114018100
1.86-1.890.3026490.30261353014179100
1.89-1.910.3095800.27911356714147100
1.91-1.940.29846820.2731132981398099
1.94-1.970.28055880.25521349914087100
1.97-20.28726180.24681356414182100
2-2.030.2646670.23361341214079100
2.03-2.070.26556550.22981338114036100
2.07-2.110.24298230.22361335314176100
2.11-2.150.23886440.20981351414158100
2.15-2.190.23746960.20671342214118100
2.19-2.240.21388070.1881334814155100
2.24-2.290.2057520.18921336714119100
2.29-2.350.21837760.1823133071408399
2.35-2.410.21025850.17621356114146100
2.41-2.480.2356550.18191340414059100
2.48-2.560.21966810.17931343514116100
2.56-2.650.20356790.16921344114120100
2.65-2.760.18316880.17241339214080100
2.76-2.890.20997000.17741348914189100
2.89-3.040.20075790.1727134261400599
3.04-3.230.19916760.17431345414130100
3.23-3.480.18456900.1698134271411799
3.48-3.830.17998120.15451320714019100
3.83-4.380.15886730.1391134341410799
4.38-5.520.17036570.145133531401099
5.52-53.80.18446530.1676134331408699
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)
10.6602-0.5368-0.19770.78940.22120.25760.03810.04860.0228-0.0764-0.0522-0.0139-0.064-0.013800.20960.0029-0.00520.2521-0.01050.21130.6571-3.2778-47.1995
20.5582-0.0817-0.27170.69130.2380.865-0.1102-0.0281-0.04910.00350.0596-0.0330.1290.0698-00.1802-0.00240.0080.2409-0.00360.208610.0699-21.5726-49.542
30.60450.10470.24350.21540.10660.3376-0.04710.05250.04960.1121-0.03450.18270.0447-0.02400.1967-0.02310.02610.2567-0.02760.3017-27.782-13.5793-38.8983
40.05580.0292-0.0310.1308-0.16720.3478-0.14940.4318-0.234-0.05030.0431-0.0174-0.0893-0.0699-0.01780.203-0.06050.06360.3885-0.120.3745-13.0427-17.7497-47.4059
50.4577-0.03530.64390.52180.0750.98590.070.1701-0.22270.0793-0.13630.30780.24380.0042-0.05770.1899-0.03630.0270.2773-0.12990.4458-37.1976-23.1979-46.1723
60.21430.20640.2520.20720.17210.2972-0.2851-0.0116-0.0577-0.5862-0.48580.8826-0.138-0.2879-0.7008-0.649-0.1995-0.51150.4236-0.36280.7658-50.871-14.5077-53.4829
70.05880.0691-0.0060.10130.07430.07690.0634-0.13710.1130.0839-0.15640.2890.0264-0.0765-0.00020.2234-0.00360.01730.2563-0.04630.3648-31.9669-12.0707-38.4201
80.27120.2303-0.26910.4524-0.24810.35470.022-0.0252-0.0223-0.0329-0.10620.042-0.0914-0.0187-0.00010.24750.0282-0.03460.2512-0.02670.238-21.805414.0569-47.4977
90.0950.0774-0.08550.2091-0.07610.0728-0.07130.0291-0.0397-0.22940.01280.17920.1591-0.118-00.3248-0.0347-0.07920.2679-0.02850.3042-31.48273.3937-55.4178
100.2450.0534-0.15520.21020.05070.313-0.02590.05960.0187-0.1356-0.00320.0581-0.1893-0.046100.38170.0115-0.0720.2627-0.00370.2338-19.988824.2862-60.8433
110.1013-0.05280.01480.11-0.01180.10440.21150.17690.2453-0.27410.01880.2323-0.5826-0.17710.00430.57920.108-0.07940.36630.04470.3428-24.268132.9834-66.3846
120.1639-0.06780.09060.0685-0.15310.1506-0.01280.1752-0.01480.03660.05880.125-0.08750.1584-0.00010.4352-0.0434-0.01930.2923-0.00730.2399-13.501519.4754-73.8946
130.09930.0013-0.01180.0624-0.07120.0979-0.04730.1028-0.0198-0.03060.02820.0167-0.18950.2688-00.4057-0.0707-0.0120.36310.01120.2607-4.01624.5214-65.2224
140.04190.01980.04960.07860.00460.05630.1310.12950.04930.0742-0.0975-0.0139-0.1888-0.0530.00010.27290.0068-0.04360.2762-0.0110.2481-18.55217.2239-47.8559
150.1624-0.1038-0.07330.0897-0.01450.0234-0.07490.19310.07880.0090.04790.004-0.1206-0.037700.24370.018-0.00130.2650.02170.2383-23.79129.5575-25.5431
160.3008-0.02810.15550.18830.0790.0915-0.2489-0.0406-0.22850.20170.1660.0860.06730.0585-0.00340.29120.08260.0150.24660.01890.2133-20.124315.4717-18.3897
170.1247-0.0561-0.04240.0492-0.0580.0665-0.3042-0.34430.09750.29140.2326-0.0131-0.0079-0.10750.00050.42020.1652-0.09830.3513-0.09190.2918-7.336421.3355-10.1302
180.1729-0.2663-0.04360.21120.00320.1238-0.2131-0.12650.18580.16160.20770.0129-0.008-0.0417-0.00080.26760.0836-0.05270.2497-0.04120.2328-21.475128.336-15.0554
190.1406-0.0687-0.01440.06210.04460.0343-0.0992-0.05790.23360.09340.0783-0.0114-0.03720.0576-0.00010.28870.08460.00930.2760.0140.2708-35.371737.8696-13.0766
200.19670.03550.02880.21150.11070.1105-0.101-0.12050.23370.08530.0890.0045-0.0231-0.05280.00090.31290.09280.04010.27990.00550.341-37.816539.3493-9.9685
210.072-0.008-0.06990.12030.04770.0439-0.1503-0.0667-0.17370.27780.12870.36720.0110.0396-0.00450.36430.09110.11110.3270.09230.3304-45.79426.3835-9.3018
220.0886-0.07210.06220.08320.01230.0587-0.03470.2089-0.02130.13870.09810.02850.0024-0.121-00.27740.03430.03290.23590.01540.2443-26.42521.9809-22.3622
230.2284-0.00360.06410.3445-0.40260.4322-0.02920.0488-0.0227-0.0802-0.0602-0.11120.0498-0.1674-0.00010.2752-0.02360.01210.2530.00440.2373-26.8951-6.2334-13.1118
240.05410.058-0.01650.12280.00620.03630.0463-0.021-0.11440.27420.0251-0.0387-0.2911-0.0613-0.00010.410.05490.03430.28830.05560.2469-31.557610.8929-7.2777
250.03530.0205-0.0110.07830.00480.01820.0463-0.12810.25130.2253-0.12340.3197-0.1899-0.2054-0.00230.31420.02310.06240.3749-0.00530.2963-34.96092.0208-3.5176
260.1856-0.05130.03480.2316-0.22360.2522-0.06110.01820.0258-0.0227-0.0137-0.06240.1214-0.1908-00.3178-0.04960.04980.25170.00140.2626-29.8811-16.47440.0609
270.08270.0547-0.10750.137-0.01490.0906-0.22270.0071-0.32510.04940.15520.20830.4847-0.4020.00110.3283-0.12110.02190.34620.01170.2836-37.3442-23.44174.6873
280.1083-0.0122-0.04940.0312-0.05420.06610.003-0.24010.0466-0.0899-0.1631-0.02260.0118-0.0900.3944-0.01340.04880.2354-0.00590.2908-21.5207-17.389811.4359
290.0034-0.00140.00440.06430.01990.00290.0114-0.4371-0.1771-0.0806-0.2717-0.19840.2930.06110.00050.40880.03790.07590.28360.05640.3632-19.1206-23.857813.819
300.06530.0173-0.02330.064-0.09260.1086-0.1988-0.054-0.0922-0.0602-0.03510.02180.26060.2044-0.00010.38760.03170.07360.2360.0310.3254-14.8021-21.08033.9521
310.04140.0343-0.05130.0503-0.01460.0707-0.1011-0.0139-0.0726-0.10860.0583-0.07260.1079-0.142100.2822-0.01750.04590.26430.0030.2841-24.8912-10.2774-12.5503
320.41150.33070.06820.35920.17370.1409-0.04620.0541-0.0208-0.00050.0420.00120.02060.012-00.23460.0037-00.2159-0.00980.23270.97793.6418-16.1404
330.07380.0774-0.02220.0243-0.02580.02970.0507-0.0927-0.0004-0.034-0.0712-0.08990.1090.0667-00.3047-0.02670.02570.28490.01520.3126-9.3888-4.1777-2.8571
340.3242-0.0808-0.05740.11490.15940.1558-0.0345-0.1295-0.04920.0599-0.0213-0.0857-0.0080.120800.3116-0.0111-0.02670.27150.00680.23774.8683.8068-7.7768
350.0331-0.02660.06460.07-0.0220.0612-0.04920.0246-0.09630.15370.0066-0.2481-0.03570.183-0.00040.3463-0.0607-0.02940.3704-0.01860.306719.488815.4916-10.028
360.2780.09650.28860.1556-0.00030.2528-0.06730.002-0.11770.11370.009-0.1818-0.20960.1067-0.00050.336-0.0379-0.06840.322-0.02120.301720.006414.4934-3.8351
370.1559-0.02020.1560.0898-0.04380.0911-0.2062-0.09060.1890.0122-0.0174-0.1064-0.54490.0434-0.00370.4869-0.0443-0.10390.2559-0.01030.343513.061427.5823-9.8903
380.1389-0.00750.07530.0232-0.01560.148-0.14670.0742-0.02930.00650.2125-0.0828-0.1228-0.037400.27770.0017-0.00640.2303-0.01180.26113.3587.1953-17.9497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 143 )A0 - 143
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 307 )A144 - 307
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 63 )B1 - 63
4X-RAY DIFFRACTION4chain 'B' and (resid 64 through 94 )B64 - 94
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 201 )B95 - 201
6X-RAY DIFFRACTION6chain 'B' and (resid 202 through 284 )B202 - 284
7X-RAY DIFFRACTION7chain 'B' and (resid 285 through 307 )B285 - 307
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 64 )C1 - 64
9X-RAY DIFFRACTION9chain 'C' and (resid 65 through 114 )C65 - 114
10X-RAY DIFFRACTION10chain 'C' and (resid 115 through 187 )C115 - 187
11X-RAY DIFFRACTION11chain 'C' and (resid 188 through 215 )C188 - 215
12X-RAY DIFFRACTION12chain 'C' and (resid 216 through 245 )C216 - 245
13X-RAY DIFFRACTION13chain 'C' and (resid 246 through 284 )C246 - 284
14X-RAY DIFFRACTION14chain 'C' and (resid 285 through 307 )C285 - 307
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 28 )D1 - 28
16X-RAY DIFFRACTION16chain 'D' and (resid 29 through 64 )D29 - 64
17X-RAY DIFFRACTION17chain 'D' and (resid 65 through 94 )D65 - 94
18X-RAY DIFFRACTION18chain 'D' and (resid 95 through 143 )D95 - 143
19X-RAY DIFFRACTION19chain 'D' and (resid 144 through 187 )D144 - 187
20X-RAY DIFFRACTION20chain 'D' and (resid 188 through 245 )D188 - 245
21X-RAY DIFFRACTION21chain 'D' and (resid 246 through 284 )D246 - 284
22X-RAY DIFFRACTION22chain 'D' and (resid 285 through 307 )D285 - 307
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 64 )E1 - 64
24X-RAY DIFFRACTION24chain 'E' and (resid 65 through 94 )E65 - 94
25X-RAY DIFFRACTION25chain 'E' and (resid 95 through 114 )E95 - 114
26X-RAY DIFFRACTION26chain 'E' and (resid 115 through 187 )E115 - 187
27X-RAY DIFFRACTION27chain 'E' and (resid 188 through 215 )E188 - 215
28X-RAY DIFFRACTION28chain 'E' and (resid 216 through 239 )E216 - 239
29X-RAY DIFFRACTION29chain 'E' and (resid 240 through 254 )E240 - 254
30X-RAY DIFFRACTION30chain 'E' and (resid 255 through 284 )E255 - 284
31X-RAY DIFFRACTION31chain 'E' and (resid 285 through 307 )E285 - 307
32X-RAY DIFFRACTION32chain 'F' and (resid 0 through 64 )F0 - 64
33X-RAY DIFFRACTION33chain 'F' and (resid 65 through 94 )F65 - 94
34X-RAY DIFFRACTION34chain 'F' and (resid 95 through 143 )F95 - 143
35X-RAY DIFFRACTION35chain 'F' and (resid 144 through 159 )F144 - 159
36X-RAY DIFFRACTION36chain 'F' and (resid 160 through 245 )F160 - 245
37X-RAY DIFFRACTION37chain 'F' and (resid 246 through 284 )F246 - 284
38X-RAY DIFFRACTION38chain 'F' and (resid 285 through 307 )F285 - 307

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