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- PDB-7np0: Crystal structure of Mycobacterium tuberculosis ArgF in complex w... -

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Basic information

Entry
Database: PDB / ID: 7np0
TitleCrystal structure of Mycobacterium tuberculosis ArgF in complex with (4-nitrophenyl)boronic acid.
ComponentsOrnithine carbamoyltransferaseOrnithine transcarbamylase
KeywordsTRANSFERASE / ArgF / Ornithine Carbamoyltransferase
Function / homology
Function and homology information


ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / arginine biosynthetic process via ornithine / 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
PHOSPHATE ION / p-nitrophenylboronic acid / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 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 26, 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)200,84419
Polymers199,2506
Non-polymers1,59413
Water27,8871548
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,43410
Polymers99,6253
Non-polymers8097
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-50 kcal/mol
Surface area31590 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4119
Polymers99,6253
Non-polymers7866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-36 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.035, 143.447, 97.526
Angle α, β, γ (deg.)90.000, 117.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ornithine carbamoyltransferase / Ornithine transcarbamylase / 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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-UKH / p-nitrophenylboronic acid / (4-nitrophenyl)boronic acid


Mass: 166.927 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H6BNO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1548 / 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: 2.86 Å3/Da / Density % sol: 57.07 %
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: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.76→70.46 Å / Num. obs: 222029 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.058 / Net I/σ(I): 16 / Num. measured all: 1149709 / Scaling rejects: 39
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
1.76-1.855.20.564167284324130.830.2720.6282.799.8
5.55-70.464.90.0473476271320.9970.0230.05336.299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.98 Å70.46 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: 1.76→70.46 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 11087 5 %
Rwork0.1618 210869 -
obs0.1628 221956 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.91 Å2 / Biso mean: 37.1847 Å2 / Biso min: 18.06 Å2
Refinement stepCycle: final / Resolution: 1.76→70.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13551 0 100 1550 15201
Biso mean--45.32 45.39 -
Num. residues----1807
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 (%)
1.76-1.780.27034050.245770137418100
1.78-1.80.26473310.227870687399100
1.8-1.820.2613820.218170007382100
1.82-1.840.23823750.209370387413100
1.84-1.870.21983700.19336879724998
1.87-1.890.19713220.1897036735899
1.89-1.920.22383360.210770597395100
1.92-1.950.24313790.210570047383100
1.95-1.980.23353960.186669897385100
1.98-2.010.20123320.179770847416100
2.01-2.050.20393600.175970617421100
2.05-2.080.19343640.173370337397100
2.08-2.120.2043610.166670157376100
2.12-2.170.20083550.16370607415100
2.17-2.210.193270.163570427369100
2.21-2.260.213490.17926939728898
2.26-2.320.1914060.165869847390100
2.32-2.380.19644100.167569987408100
2.38-2.450.18723790.164269987377100
2.45-2.530.19093350.163170757410100
2.53-2.620.18193640.161370927456100
2.62-2.730.19173850.166270157400100
2.73-2.850.18183910.169770097400100
2.85-30.19974230.163569977420100
3-3.190.18413850.158270477432100
3.19-3.440.15553680.154870457413100
3.44-3.780.16273660.150870857451100
3.78-4.330.14893950.1387027742299
4.33-5.460.15473940.14387041743599
5.46-70.460.18973420.16317136747899
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)
12.8641-1.5348-0.74052.46940.12651.99470.0020.0884-0.032-0.01-0.00930.0474-0.0309-0.02030.01410.1906-0.0227-0.02150.1963-0.02860.20070.2775-4.6496-41.4939
23.25861.57580.1344.6366-1.65292.6157-0.29480.8303-0.1863-1.01450.18-0.24220.173-0.01350.08350.35660.02740.03030.3774-0.04670.2546-5.29835.7912-55.2341
31.9714-1.5751-0.01192.83480.47941.27750.130.19480.029-0.371-0.1148-0.0895-0.07840.0253-0.00870.1993-0.0040.00540.267-0.01740.20674.5776-6.3483-49.6189
42.1238-0.0298-0.49932.58480.765.3689-0.0968-0.1689-0.18850.07710.1259-0.18920.22580.48120.02530.18390.01660.00750.2976-0.01060.299114.3454-22.0148-46.2941
51.6310.66740.1682.1090.50761.667-0.05660.0319-0.0357-0.12550.0955-0.27330.03190.1893-0.04930.19780.0150.03270.29-0.01420.268116.1498-19.731-51.6441
61.79270.45760.25392.942-1.87095.3696-0.16140.0525-0.0441-0.36790.34390.26790.2956-0.5546-0.08670.3291-0.05960.03290.3445-0.02080.33926.9753-27.4312-65.4464
73.3249-0.311-1.10714.35391.87622.8349-0.2874-0.027-0.24230.1490.0090.15670.42060.01890.26750.2997-0.01880.05420.24230.01230.28934.2941-31.2409-47.3743
81.7552-0.5441-0.76227.0089-0.37322.4448-0.0793-0.13280.01870.24660.0831-0.1232-0.06510.001-0.01050.16080.011-0.01390.2653-0.01420.20141.2106-8.8983-39.6868
94.1760.72010.66462.28030.45661.5355-0.03350.3705-0.4326-0.18230.0437-0.01130.08870.0770.0350.197-0.01260.0020.2373-0.03240.2678-25.558-16.9894-42.8024
104.66490.95121.34491.93250.61322.0188-0.06670.5763-0.2204-0.2087-0.03970.46050.0547-0.18510.09340.1897-0.0193-0.01630.3658-0.09560.4472-45.5524-18.7759-48.7568
110.97280.0985-0.09352.638-0.35221.99490.00510.02710.04750.03230.0290.2414-0.1803-0.1525-0.01930.21280.01-0.00950.2564-0.02440.2476-23.909715.7144-46.9588
122.31970.2208-0.99421.1627-1.07441.2265-0.08790.3959-0.3215-0.36830.08490.12040.4341-0.11210.00590.2938-0.0125-0.05370.2435-0.03830.253-22.20672.3527-53.0287
131.09830.7921-0.35532.9554-0.93562.1157-0.04690.148-0.005-0.25870.08870.2660.0742-0.2923-0.06310.25980.0173-0.05480.2824-0.02480.2709-27.761311.8725-55.1498
143.01241.11470.65273.91680.77675.0511-0.07060.17690.3240.05290.03350.1332-0.49640.04320.06840.3705-0.0179-0.03120.24820.02140.277-16.503529.5624-63.1253
152.585-0.0015-0.97362.00290.12563.5780.00620.28140.1813-0.21940.01310.1666-0.3864-0.2922-0.03440.38450.0096-0.07030.28360.04270.2535-21.018727.9055-66.8303
165.71713.87911.60036.46432.67773.17680.04310.2143-0.42690.29120.2617-0.30140.38890.494-0.18240.4547-0.0199-0.05370.37160.01250.2889-14.435316.8197-79.6066
173.31750.1754-0.5242.0038-1.17144.1139-0.12960.10980.0016-0.12870.0052-0.2424-0.08680.48430.09350.3351-0.0236-0.00710.34290.01230.2778-4.432424.0327-65.5913
185.54071.185-2.23422.2411-1.11833.82120.0361-0.04910.20740.07260.02740.0535-0.1415-0.0538-0.06270.27780.0089-0.04840.2136-0.01540.2333-18.726516.9204-48.0602
192.7285-0.26830.16843.2013-0.10481.4818-0.06130.25790.2611-0.0990.0685-0.1545-0.22830.03660.0290.26360.03920.02570.27460.03230.2525-24.259529.2274-25.9515
202.3957-0.43591.10052.63780.95362.417-0.0572-0.162-0.19330.26980.1568-0.12380.08060.1046-0.0680.2380.02620.0130.23290.0170.2118-17.876515.7526-20.5837
212.2770.0973-0.81082.02680.16521.1911-0.0698-0.59710.01370.72470.1243-0.12240.07360.1441-0.13850.41830.0927-0.00770.31570.00280.24-16.413717.1147-11.2122
223.5283-1.22580.48981.4765-0.11141.2694-0.1502-0.37430.33060.30180.1964-0.1213-0.13280.0072-0.04560.32850.0635-0.02430.2593-0.03150.2606-18.003627.4968-15.2412
233.8933-0.5388-0.32622.48610.37572.4244-0.1708-0.42250.39120.34130.2119-0.041-0.2824-0.09-0.02470.3360.12370.02630.27550.00240.3035-35.367537.8305-13.4714
243.1905-0.1868-0.44442.04910.62362.4392-0.1546-0.49470.45260.40570.2287-0.0177-0.1825-0.0818-0.0630.38870.17340.01510.3346-0.01610.3836-37.493439.6026-10.9024
251.711-0.5984-0.63472.72610.46831.5251-0.3569-0.6072-0.32140.69330.29870.39520.06670.08580.01850.39120.15110.14780.45530.13780.3995-45.713926.3349-9.2351
267.00680.4399-1.99993.1288-0.09272.80980.18870.12380.01330.16510.04510.2232-0.2995-0.1691-0.26150.24130.05560.00710.18480.01980.1801-26.602821.7624-22.4372
271.23290.3989-0.64872.4607-0.69143.0945-0.08020.12940.0234-0.16080.09160.04270.2322-0.2858-0.01010.2301-0.01310.00170.25040.01330.2259-27.0809-6.3815-12.966
281.1816-0.8098-0.47043.0491-0.77852.24540.045-0.22780.17210.51030.12040.2738-0.5972-0.5272-0.15920.40720.05710.05620.41270.01110.332-33.1536.9472-5.5396
291.0085-0.0208-0.25821.5644-1.38812.9729-0.12190.1109-0.1156-0.17010.10170.08740.4815-0.44290.02260.307-0.10230.03710.2631-0.01140.2492-32.053-17.3940.3356
303.35020.3012-0.23441.3921-0.85083.6993-0.1469-0.1296-0.2278-0.1728-0.0592-0.11170.48320.20260.15780.34680.0130.06910.17130.03530.2603-19.9648-22.38848.4751
313.4428-1.51431.26923.2182-1.99183.9256-0.06120.0045-0.0713-0.38450.0722-0.06250.3302-0.3364-0.04270.295-0.07170.06090.2467-0.00080.257-24.9885-10.534-12.4813
322.77990.10990.25871.3216-0.18262.4347-0.0595-0.0016-0.13090.04430.0745-0.053-0.0315-0.0213-0.02920.2435-0.01110.00630.1572-0.01360.22180.84063.4053-16.1248
332.54150.1024-0.19734.2031-3.01162.1991-0.0777-0.72250.08410.905-0.0404-0.302-0.146-0.12660.03670.5168-0.0235-0.00070.4027-0.00260.3411-9.2412-4.3254-2.6735
343.0861.8326-0.18172.44360.23431.6990.0914-0.2952-0.07190.2961-0.0911-0.08990.03560.06740.0130.29730.0094-0.02090.26430.00590.25784.85993.5494-7.8301
352.7330.53331.18852.86270.77213.2724-0.0194-0.0897-0.07150.16350.0588-0.2312-0.18490.1831-0.05230.2889-0.0669-0.05070.2746-0.00230.287619.77214.5065-4.8125
363.06790.85761.21562.88270.58841.9868-0.21090.01820.1545-0.01980.0037-0.0153-0.3015-0.02390.18280.4423-0.0408-0.06180.23710.00160.320112.979627.3475-9.9024
373.56621.55890.53736.9215-0.53582.9644-0.1840.1214-0.06240.07640.3148-0.0611-0.0354-0.0645-0.12160.18460.0036-0.00070.2384-0.01590.18213.26637.1468-17.9655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 64 )A0 - 64
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 94 )A65 - 94
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 143 )A95 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 159 )A144 - 159
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 231 )A160 - 231
6X-RAY DIFFRACTION6chain 'A' and (resid 232 through 245 )A232 - 245
7X-RAY DIFFRACTION7chain 'A' and (resid 246 through 284 )A246 - 284
8X-RAY DIFFRACTION8chain 'A' and (resid 285 through 307 )A285 - 307
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 143 )B1 - 143
10X-RAY DIFFRACTION10chain 'B' and (resid 144 through 307 )B144 - 307
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 50 )C1 - 50
12X-RAY DIFFRACTION12chain 'C' and (resid 51 through 83 )C51 - 83
13X-RAY DIFFRACTION13chain 'C' and (resid 84 through 143 )C84 - 143
14X-RAY DIFFRACTION14chain 'C' and (resid 144 through 159 )C144 - 159
15X-RAY DIFFRACTION15chain 'C' and (resid 160 through 231 )C160 - 231
16X-RAY DIFFRACTION16chain 'C' and (resid 232 through 245 )C232 - 245
17X-RAY DIFFRACTION17chain 'C' and (resid 246 through 284 )C246 - 284
18X-RAY DIFFRACTION18chain 'C' and (resid 285 through 307 )C285 - 307
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 28 )D1 - 28
20X-RAY DIFFRACTION20chain 'D' and (resid 29 through 50 )D29 - 50
21X-RAY DIFFRACTION21chain 'D' and (resid 51 through 83 )D51 - 83
22X-RAY DIFFRACTION22chain 'D' and (resid 84 through 143 )D84 - 143
23X-RAY DIFFRACTION23chain 'D' and (resid 144 through 187 )D144 - 187
24X-RAY DIFFRACTION24chain 'D' and (resid 188 through 245 )D188 - 245
25X-RAY DIFFRACTION25chain 'D' and (resid 246 through 284 )D246 - 284
26X-RAY DIFFRACTION26chain 'D' and (resid 285 through 307 )D285 - 307
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 64 )E1 - 64
28X-RAY DIFFRACTION28chain 'E' and (resid 65 through 114 )E65 - 114
29X-RAY DIFFRACTION29chain 'E' and (resid 115 through 201 )E115 - 201
30X-RAY DIFFRACTION30chain 'E' and (resid 202 through 284 )E202 - 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 245 )F144 - 245
36X-RAY DIFFRACTION36chain 'F' and (resid 246 through 284 )F246 - 284
37X-RAY DIFFRACTION37chain 'F' and (resid 285 through 307 )F285 - 307

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