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

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Basic information

Entry
Database: PDB / ID: 7nou
TitleCrystal structure of Mycobacterium tuberculosis ArgF in complex with (3,5-dichlorophenyl)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
Chem-NMR / PHOSPHATE ION / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 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)201,71821
Polymers199,2506
Non-polymers2,46815
Water18,0331001
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,95411
Polymers99,6253
Non-polymers1,3298
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-33 kcal/mol
Surface area31100 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,76410
Polymers99,6253
Non-polymers1,1397
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-35 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.299, 144.662, 97.756
Angle α, β, γ (deg.)90.000, 117.800, 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-NMR / [3,5-bis(chloranyl)phenyl]-oxidanyl-oxidanylidene-boron


Mass: 189.812 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H4BCl2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1001 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
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-F / 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: 1.98→86.47 Å / Num. obs: 157930 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rrim(I) all: 0.091 / Net I/σ(I): 16.1 / Num. measured all: 1604954 / Scaling rejects: 531
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
1.98-2.08100.937230134230550.8010.3090.9882.7100
6.25-86.479.50.0484842250890.9980.0160.0541.599.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.03 Å86.47 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: 1.98→86.47 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 8007 5.07 %
Rwork0.1745 149849 -
obs0.1759 157856 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.9 Å2 / Biso mean: 43.3589 Å2 / Biso min: 20.82 Å2
Refinement stepCycle: final / Resolution: 1.98→86.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 141 1001 14622
Biso mean--54.75 48.33 -
Num. residues----1801
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 (%)
1.98-20.29972800.264649925272100
2-2.020.27052600.24849515211100
2.02-2.050.26142610.237650365297100
2.05-2.070.25932960.230749105206100
2.07-2.10.28182830.224449765259100
2.1-2.130.24372160.211750475263100
2.13-2.160.26062700.209149715241100
2.16-2.190.22512910.200549835274100
2.19-2.230.25042860.197949295215100
2.23-2.260.28172610.24334943520499
2.26-2.30.22422730.200949945267100
2.3-2.340.24242820.19549635245100
2.34-2.390.22032620.187849955257100
2.39-2.440.19822740.175549825256100
2.44-2.490.21412900.180949555245100
2.49-2.550.21792540.180750115265100
2.55-2.610.20842160.175950225238100
2.61-2.680.2012860.173649945280100
2.68-2.760.21682280.184550225250100
2.76-2.850.20532910.189249675258100
2.85-2.950.20982570.183950205277100
2.95-3.070.22492330.186150705303100
3.07-3.210.22722360.179749905226100
3.21-3.380.19482990.179849695268100
3.38-3.590.19622680.171650015269100
3.59-3.870.19582420.159350465288100
3.87-4.260.16722590.142350385297100
4.26-4.880.16122980.139549905288100
4.88-6.140.18172800.165850125292100
6.14-86.470.17222750.16085070534599
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)
11.8884-0.68860.00431.92240.12681.3245-0.0476-0.09120.11470.09990.0443-0.0425-0.06050.0945-0.01830.2369-0.008-0.0150.2325-0.02660.25390.3118-4.909-41.3284
21.62530.717-0.14192.426-0.91240.5555-0.18220.6048-0.3313-0.7410.2671-0.16550.0243-0.1022-0.08580.4646-0.0427-0.0030.4453-0.08170.3195-5.50965.2125-55.6854
31.5891-0.5348-0.34921.45440.42410.7658-0.02280.0896-0.0085-0.0944-0.0234-0.1680.0110.09110.01660.2244-0.0133-0.00020.2771-0.02390.26096.9954-10.2505-48.471
41.53010.3874-0.37161.87180.57542.2307-0.13680.0517-0.1164-0.07260.1122-0.22470.10830.20150.01570.22210.01780.03790.2842-0.0170.337814.2309-22.8729-53.2229
51.0933-1.1277-0.96972.30980.61821.3266-0.1368-0.0857-0.19870.2095-0.0018-0.01120.2171-0.09070.07630.2355-0.00840.00560.2832-0.01670.30012.1356-20.0281-43.1421
63.1916-0.15990.53411.80080.26021.37860.024-0.3551-0.93730.1753-0.02410.0970.1306-0.1545-0.0120.2033-0.04580.02090.32990.09710.5669-27.9224-13.9587-38.3639
71.3378-1.1322-0.17521.5983-0.30570.58930.22560.4708-0.5486-0.57130.01390.29640.4497-0.128-0.16570.4332-0.0259-0.0650.4977-0.04980.6004-12.9067-19.2346-48.198
84.39271.02270.85791.49840.87341.6096-0.05720.5706-1.3514-0.1655-0.1060.2684-0.0982-0.16630.12360.1202-0.0575-0.01340.3806-0.13061.0065-42.8598-20.3607-48.5339
92.4759-0.10830.26932.15170.24942.07960.2052-0.6223-0.80870.00360.08050.37360.0217-0.17740.07050.2561-0.0530.00940.39140.10720.5502-32.2384-12.4126-38.0744
102.057-0.0935-0.24892.1983-0.29651.45780.0172-0.0852-0.0293-0.0372-0.03730.2933-0.1898-0.1290.03950.26040.0107-0.02120.2653-0.02090.2432-21.945413.6214-47.3451
112.79850.3322-0.06221.2793-0.660.5198-0.04760.5818-0.0324-0.68150.0120.21530.0854-0.32160.04440.4447-0.0049-0.07360.3904-0.0080.4121-31.7042-1.0025-53.5849
121.32760.4635-0.13931.6497-0.82621.0911-0.0590.16980.0631-0.30190.02980.2652-0.0213-0.11190.03230.34910.0115-0.05260.2772-0.02550.2997-23.219617.9468-57.5499
131.45010.50640.02411.0135-0.33352.6402-0.07760.27070.2138-0.27480.11080.1972-0.2785-0.1549-0.00860.4378-0.0117-0.07020.29710.06080.2995-18.016226.3548-68.9129
141.14840.6664-0.47951.3527-1.12322.26920.03040.01970.0369-0.003-0.071-0.1103-0.18930.23420.04390.3472-0.0167-0.04040.2738-0.01590.2705-11.137419.7847-56.1528
151.8317-0.7307-0.46191.43190.16411.2655-0.11270.1226-0.00860.13350.0772-0.0083-0.244-0.19450.02910.37910.10960.01780.38810.05910.2481-22.111821.7248-21.413
161.8881-0.9898-0.12361.16750.36950.8437-0.1978-0.27920.3180.3630.2227-0.1252-0.2515-0.1352-0.0280.51210.1366-0.03150.39370.05170.2853-16.943225.9778-14.0026
172.5008-0.5604-0.46021.61210.65541.5713-0.0294-0.16740.10490.23940.05240.2399-0.1969-0.17060.00290.51350.22960.08540.44990.11490.3354-39.52635.3854-11.415
182.9239-0.261-0.62331.76290.20261.84280.26820.18190.16570.20880.0490.1358-0.3623-0.3071-0.11520.40130.13830.04370.44040.07410.2688-26.62421.9049-22.1382
191.365-0.14-0.23812.7014-1.10591.75570.03270.04420.11630.21980.10290.247-0.1398-0.5316-0.12530.32580.00780.01070.43150.06670.3133-29.6173-0.842-9.483
201.13680.2798-0.40021.2755-1.15153.0429-0.09360.0789-0.0465-0.14570.04930.08670.4651-0.18640.06680.3636-0.06790.03240.2883-0.00020.3243-26.3764-18.36332.1577
211.8109-0.72640.26131.35830.11271.7255-0.1320.0956-0.3428-0.02850.1469-0.18250.13120.2532-0.05740.3372-0.01330.02060.309-0.03420.35649.44050.9509-16.9307
221.7202-0.3037-0.0891.4305-0.28752.8123-0.0446-0.0357-0.0311-0.14470.14230.16620.06130.1958-0.10230.28580.0140.02330.29490.02850.2402-6.20372.9512-15.3334
230.68260.5190.29671.9519-0.09310.06330.0262-0.4382-0.07110.5890.01960.1031-0.2994-0.2346-0.01280.43130.0450.05080.44770.03470.2884-8.15044.8689-6.7579
241.46760.5998-0.75740.7257-0.47180.36380.083-0.5626-0.45250.1707-0.2215-0.28050.14860.25810.10330.44760.04220.03620.41520.08860.3329-2.4432-4.9311-2.4384
251.47390.5180.44711.29740.43921.2624-0.13150.0418-0.06440.08580.1036-0.1004-0.40960.18930.05170.3545-0.022-0.00850.29080.02010.233111.724810.5892-10.7531
261.26060.12740.27381.11140.45391.6874-0.04980.1396-0.14040.0998-0.0145-0.3594-0.38390.41280.0580.4216-0.0762-0.04650.36740.01620.308921.616312.2217-5.4756
271.285-0.10910.921.42531.04913.3362-0.4634-0.4430.47980.476-0.13110.8701-0.387-0.98650.10030.73020.0094-0.09130.5152-0.03110.460613.036624.21163.9448
281.2110.28850.87382.1530.06391.299-0.24970.0540.10420.00440.0821-0.022-0.5027-0.0060.13230.6233-0.0493-0.08850.31310.00090.326813.04527.5737-9.6605
292.14110.3046-0.00492.9265-0.13711.8966-0.19660.1388-0.07770.23980.207-0.2184-0.115-0.01150.08160.3173-0.00050.00140.2619-0.01650.24973.26217.231-17.4534
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 159 )A95 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 254 )A160 - 254
5X-RAY DIFFRACTION5chain 'A' and (resid 255 through 307 )A255 - 307
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 64 )B1 - 64
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 94 )B65 - 94
8X-RAY DIFFRACTION8chain 'B' and (resid 95 through 284 )B95 - 284
9X-RAY DIFFRACTION9chain 'B' and (resid 285 through 307 )B285 - 307
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 64 )C1 - 64
11X-RAY DIFFRACTION11chain 'C' and (resid 65 through 94 )C65 - 94
12X-RAY DIFFRACTION12chain 'C' and (resid 95 through 159 )C95 - 159
13X-RAY DIFFRACTION13chain 'C' and (resid 160 through 254 )C160 - 254
14X-RAY DIFFRACTION14chain 'C' and (resid 255 through 307 )C255 - 307
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 63 )D1 - 63
16X-RAY DIFFRACTION16chain 'D' and (resid 64 through 143 )D64 - 143
17X-RAY DIFFRACTION17chain 'D' and (resid 144 through 284 )D144 - 284
18X-RAY DIFFRACTION18chain 'D' and (resid 285 through 307 )D285 - 307
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 114 )E1 - 114
20X-RAY DIFFRACTION20chain 'E' and (resid 115 through 307 )E115 - 307
21X-RAY DIFFRACTION21chain 'F' and (resid 0 through 28 )F0 - 28
22X-RAY DIFFRACTION22chain 'F' and (resid 29 through 50 )F29 - 50
23X-RAY DIFFRACTION23chain 'F' and (resid 51 through 83 )F51 - 83
24X-RAY DIFFRACTION24chain 'F' and (resid 84 through 114 )F84 - 114
25X-RAY DIFFRACTION25chain 'F' and (resid 115 through 159 )F115 - 159
26X-RAY DIFFRACTION26chain 'F' and (resid 160 through 223 )F160 - 223
27X-RAY DIFFRACTION27chain 'F' and (resid 224 through 245 )F224 - 245
28X-RAY DIFFRACTION28chain 'F' and (resid 246 through 284 )F246 - 284
29X-RAY DIFFRACTION29chain 'F' and (resid 285 through 307 )F285 - 307

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