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

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Basic information

Entry
Database: PDB / ID: 7nnz
TitleCrystal structure of Mycobacterium tuberculosis ArgF in complex with 5-methyl-4-phenylthiazol-2-amine.
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
PHOSPHATE ION / 5-methyl-4-phenyl-1,3-thiazol-2-amine / Ornithine carbamoyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 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)201,05620
Polymers199,2506
Non-polymers1,80614
Water33,3641852
1
A: Ornithine carbamoyltransferase
B: Ornithine carbamoyltransferase
C: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2908
Polymers99,6253
Non-polymers6655
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-40 kcal/mol
Surface area31600 Å2
MethodPISA
2
D: Ornithine carbamoyltransferase
E: Ornithine carbamoyltransferase
F: Ornithine carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,76612
Polymers99,6253
Non-polymers1,1419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-66 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.617, 143.002, 97.591
Angle α, β, γ (deg.)90.000, 117.580, 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.: 9 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PTZ / 5-methyl-4-phenyl-1,3-thiazol-2-amine / 2-Amino-5-methyl-4-phenylthiazole


Mass: 190.265 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H10N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1852 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.68→81.2 Å / Num. obs: 252690 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.047 / Rrim(I) all: 0.108 / Net I/σ(I): 9.3 / Num. measured all: 1305874 / Scaling rejects: 489
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
1.68-1.774.40.988162377368250.4560.531.1281.799.8
5.31-81.25.10.0674121080750.9940.0310.07420.398.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.97 Å81.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.3data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P2G
Resolution: 1.68→48.96 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1827 12793 5.06 %
Rwork0.1668 239824 -
obs0.1676 252617 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.41 Å2 / Biso mean: 27.8882 Å2 / Biso min: 12.49 Å2
Refinement stepCycle: final / Resolution: 1.68→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13603 0 110 1854 15567
Biso mean--36.2 38.72 -
Num. residues----1811
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 (%)
1.68-1.70.28963780.280380358413100
1.7-1.720.30244370.270479028339100
1.72-1.740.26684280.254379408368100
1.74-1.760.2623850.245880438428100
1.76-1.780.27734320.237779698401100
1.78-1.810.25293890.21980468435100
1.81-1.830.23074080.215979878395100
1.83-1.860.24684410.215879458386100
1.86-1.890.25034060.215779988404100
1.89-1.920.2354360.198179728408100
1.92-1.950.23284100.187180168426100
1.95-1.990.21264040.179780228426100
1.99-2.030.20334570.173479008357100
2.03-2.070.2064340.17479818415100
2.07-2.120.19513730.168580308403100
2.12-2.160.17974860.162579278413100
2.16-2.220.1874400.161779898429100
2.22-2.280.18754010.162880338434100
2.28-2.350.17674070.163180208427100
2.35-2.420.19074540.161379688422100
2.42-2.510.18244700.162179638433100
2.51-2.610.17824400.160679878427100
2.61-2.730.19874470.162279738420100
2.73-2.870.1944820.169279628444100
2.87-3.050.16853910.161580668457100
3.05-3.290.17013890.158180428431100
3.29-3.620.163980.155580708468100
3.62-4.140.13684470.136579978444100
4.14-5.210.13814650.136480048469100
5.21-48.960.18674580.17348037849599
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)
10.4658-0.34-0.31520.44210.26090.29140.0420.07110.0126-0.0397-0.03920.0072-0.0679-0.0215-00.14160.0033-0.0110.1784-0.00310.15250.7165-3.4379-47.4976
20.40640.0915-0.26910.46830.10430.5611-0.07-0.0122-0.0453-0.01950.0502-0.0270.0820.0587-00.13220.00310.00140.1799-0.00750.161810.2575-21.7832-49.7635
30.08320.01380.03030.0169-0.01170.0241-0.0506-0.1491-0.10830.1259-0.09160.21570.1297-0.1574-0.00010.1797-0.03050.05680.1956-0.02670.2714-32.5651-20.1599-35.3578
40.0920.1121-0.01520.10520.02230.035-0.03070.06420.0676-0.011-0.02060.1481-0.0779-0.0085-00.1419-0.0015-0.00690.189-0.00680.2077-23.4504-8.4924-42.024
50.06340.0296-0.01930.0519-0.02920.0069-0.08580.2441-0.1945-0.11250.02880.0688-0.0144-0.0185-00.1846-0.02240.02850.2876-0.05960.2756-12.737-18.3215-49.1109
60.16080.13530.03090.1921-0.13610.5408-0.05940.0908-0.0990.0369-0.05020.11010.13530.0046-0.05590.1423-0.01030.01090.1921-0.06940.2532-28.9934-19.982-45.5953
70.0601-0.06830.06590.1535-0.10680.0790.10650.0358-0.1361-0.0288-0.25440.36860.1762-0.12440.02520.1121-0.07450.01220.3435-0.19180.4684-45.3214-23.8897-48.5718
80.06830.00830.02070.00520.00090.00470.2262-0.1001-0.1946-0.0155-0.0310.04080.12190.01060.06220.0576-0.40710.0321-0.0921-0.24390.6232-42.3331-33.5346-42.9464
90.04570.0144-0.02190.0151-0.00160.0081-0.049-0.0613-0.06590.0037-0.15470.14110.0129-0.0967-0.0898-0.3823-0.2744-0.12390.3885-0.39610.6793-54.338-25.5549-51.0577
100.02030.0040.01170.06570.01360.02930.060.0034-0.018-0.1485-0.10180.29320.0241-0.0258-0.01220.20.021-0.08680.3456-0.16610.429-48.2455-17.6857-57.9537
110.1915-0.0424-0.02750.0290.01230.0403-0.212-0.03370.13-0.1328-0.1590.5034-0.1242-0.1568-0.20660.03540.0895-0.28840.4402-0.24130.5162-50.3634-9.464-53.4068
120.0310.03490.01350.06680.04520.0370.0227-0.0466-0.0180.0657-0.10950.21580.0669-0.0665-0.00880.1514-0.00290.00290.1863-0.03530.2479-31.7869-12.2023-38.5881
130.3250.0687-0.12140.4565-0.34060.4292-0.0040.0248-0.0216-0.1301-0.00420.05150.0383-0.0181-00.20280.0041-0.03020.1766-0.02130.1727-24.71311.0612-51.9391
140.18440.0382-0.00930.0783-0.13470.1760.05530.10790.0447-0.088-0.03780.0319-0.2343-0.0741-00.30830.0238-0.02850.22330.01920.1838-19.609928.179-66.2147
150.0506-0.03980.03720.0214-0.02220.00560.07820.0682-0.0955-0.0762-0.0445-0.00220.02660.15770.00010.352-0.0229-0.01560.33220.02450.2164-9.938721.6503-76.2426
160.04640.0046-0.01030.025-0.04810.0677-0.03980.11780.033-0.0461-0.0517-0.0422-0.06440.2638-00.2704-0.02910.00120.29990.01770.2105-4.161222.6262-63.9362
170.02810.01410.04180.0552-0.00120.06280.03060.09890.0885-0.0046-0.02280.0287-0.1105-0.0131-00.18860.0118-0.01780.1958-0.00610.1783-18.499416.9488-47.8928
180.3126-0.10160.00410.1650.08030.1421-0.05470.0424-0.01650.070.07520.0263-0.002-0.01500.17790.02880.00690.17510.01480.1588-21.684821.6317-21.5175
190.21-0.2324-0.11720.4102-0.03540.1467-0.0566-0.08780.0540.15910.1063-0.0138-0.0067-0.0182-0.00090.20910.0616-0.02210.1861-0.01490.1714-19.973527.055-13.5084
200.07020.0151-0.04540.025-0.00750.03850.0093-0.02740.2220.06440.0982-0.0424-0.14180.041100.24780.05160.03090.19880.00460.2241-32.451241.4569-14.2553
210.0330.06110.00850.05940.02590.0207-0.0511-0.01830.11420.1202-0.00840.20750.0725-0.0374-00.24680.09190.07560.22690.02130.2062-42.361334.9122-5.4455
220.0221-0.0014-0.01770.07520.06130.0405-0.1507-0.0878-0.14390.26340.11810.31110.06480.0004-0.0010.25610.07690.1040.2380.06420.2499-45.595426.0221-9.0264
230.0369-0.0403-0.00430.03750.00070.0188-0.02530.05-0.00540.08090.06840.0015-0.0098-0.02040.00010.18970.02590.01740.17970.01610.1784-26.359921.705-22.2876
240.0064-0.01350.01630.0747-0.0780.0506-0.02030.1394-0.0213-0.0717-0.01590.00770.2425-0.293100.21-0.04440.00720.2598-0.00340.1758-33.0819-12.8695-12.9065
250.15450.1205-0.10230.244-0.27020.1805-0.03460.0466-0.01130.12830.0174-0.0266-0.1147-0.0261-0.00420.25380.02080.00770.15780.0180.1662-25.78164.0498-10.3372
260.07480.0320.00940.1012-0.14610.3597-0.02890.04280.0033-0.00450.0015-0.04550.0406-0.2221-0.00050.231-0.01710.03550.20440.00180.1765-30.793-12.4637-0.8089
270.053-0.024-0.06640.12670.02010.0872-0.13210.0382-0.2224-0.00040.06020.01880.4034-0.2603-0.00680.289-0.09420.03710.2276-0.00440.2101-34.1418-24.35224.3079
280.17640.0530.01640.0464-0.08480.1195-0.073-0.0731-0.0196-0.0291-0.1095-0.02580.12770.1815-0.00050.27050.01010.04580.19140.01910.2147-16.7653-20.28148.9947
290.03570.0083-0.04570.0179-0.00820.0548-0.1038-0.0808-0.0481-0.06040.04-0.05420.1244-0.1343-00.2009-0.02150.02940.2114-0.00430.1995-24.7573-10.4629-12.6818
300.07790.0467-0.03340.05290.02250.038-0.030.0609-0.0496-0.04440.0391-0.1510.02350.1472-0.00010.17580.00450.00120.1641-0.02310.21749.4640.6212-17.2924
310.43930.12690.22660.30350.25630.25640.0311-0.09060.01590.088-0.05320.00890.0243-0.070100.1883-0.01550.00720.17190.00340.1604-2.12512.4501-8.9635
320.38170.14330.38420.29220.05370.3645-0.0672-0.027-0.02150.05780.0204-0.1474-0.15840.1043-00.2465-0.0174-0.04420.207-0.01440.237917.800818.2284-6.1359
330.0606-0.00420.04190.0218-0.01540.0528-0.05580.0034-0.0240.0490.0535-0.0863-0.048-0.02080.00010.18370.0074-0.00650.1643-0.00990.1973.40666.9278-18.1044
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 28 )B1 - 28
4X-RAY DIFFRACTION4chain 'B' and (resid 29 through 64 )B29 - 64
5X-RAY DIFFRACTION5chain 'B' and (resid 65 through 94 )B65 - 94
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 143 )B95 - 143
7X-RAY DIFFRACTION7chain 'B' and (resid 144 through 187 )B144 - 187
8X-RAY DIFFRACTION8chain 'B' and (resid 188 through 201 )B188 - 201
9X-RAY DIFFRACTION9chain 'B' and (resid 202 through 215 )B202 - 215
10X-RAY DIFFRACTION10chain 'B' and (resid 216 through 245 )B216 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid 246 through 284 )B246 - 284
12X-RAY DIFFRACTION12chain 'B' and (resid 285 through 307 )B285 - 307
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 143 )C1 - 143
14X-RAY DIFFRACTION14chain 'C' and (resid 144 through 231 )C144 - 231
15X-RAY DIFFRACTION15chain 'C' and (resid 232 through 254 )C232 - 254
16X-RAY DIFFRACTION16chain 'C' and (resid 255 through 284 )C255 - 284
17X-RAY DIFFRACTION17chain 'C' and (resid 285 through 307 )C285 - 307
18X-RAY DIFFRACTION18chain 'D' and (resid 0 through 64 )D0 - 64
19X-RAY DIFFRACTION19chain 'D' and (resid 65 through 159 )D65 - 159
20X-RAY DIFFRACTION20chain 'D' and (resid 160 through 208 )D160 - 208
21X-RAY DIFFRACTION21chain 'D' and (resid 209 through 245 )D209 - 245
22X-RAY DIFFRACTION22chain 'D' and (resid 246 through 284 )D246 - 284
23X-RAY DIFFRACTION23chain 'D' and (resid 285 through 307 )D285 - 307
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 28 )E1 - 28
25X-RAY DIFFRACTION25chain 'E' and (resid 29 through 94 )E29 - 94
26X-RAY DIFFRACTION26chain 'E' and (resid 95 through 187 )E95 - 187
27X-RAY DIFFRACTION27chain 'E' and (resid 188 through 223 )E188 - 223
28X-RAY DIFFRACTION28chain 'E' and (resid 224 through 284 )E224 - 284
29X-RAY DIFFRACTION29chain 'E' and (resid 285 through 307 )E285 - 307
30X-RAY DIFFRACTION30chain 'F' and (resid 0 through 28 )F0 - 28
31X-RAY DIFFRACTION31chain 'F' and (resid 29 through 143 )F29 - 143
32X-RAY DIFFRACTION32chain 'F' and (resid 144 through 284 )F144 - 284
33X-RAY DIFFRACTION33chain 'F' and (resid 285 through 307 )F285 - 307

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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