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- PDB-7nnc: Crystal structure of Mycobacterium tuberculosis ArgD with prosthe... -

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Basic information

Entry
Database: PDB / ID: 7nnc
TitleCrystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal-5'-phosphate and 6-Methoxyquinoline-3-carboxylic acid
ComponentsAcetylornithine aminotransferase
KeywordsTRANSFERASE / ArgD / N-acetylornithine aminotrasferase / AcOAT
Function / homology
Function and homology information


acetylornithine transaminase / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / L-arginine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytoplasm
Similarity search - Function
Acetylornithine/Succinylornithine transaminase family / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
NITRATE ION / 6-methoxyquinoline-3-carboxylic acid / Acetylornithine aminotransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGupta, P. / Mendes, V. / 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 24, 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: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,6277
Polymers165,3004
Non-polymers3273
Water28,9501607
1
A: Acetylornithine aminotransferase
B: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7123
Polymers82,6502
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-63 kcal/mol
Surface area23690 Å2
MethodPISA
2
C: Acetylornithine aminotransferase
D: Acetylornithine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,9154
Polymers82,6502
Non-polymers2652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-62 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.461, 184.944, 71.578
Angle α, β, γ (deg.)90.000, 106.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetylornithine aminotransferase / ACOAT


Mass: 41325.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: argD, Rv1655, MTCY06H11.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WPZ7, acetylornithine transaminase
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-UMH / 6-methoxyquinoline-3-carboxylic acid


Mass: 203.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1607 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-Tris Propane pH 8.5 18% PEG Smear High (PEGs 6K, 8K, 10K) 0.2 M ammonium nitrate 10 mM nickel chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→68.78 Å / Num. obs: 177420 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.014 / Rrim(I) all: 0.033 / Net I/σ(I): 34 / Num. measured all: 948793
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
1.7-1.734.90.0894117484570.9940.0440.112.195.6
9.31-68.7850.029531410710.9980.0140.03258.996.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.93 Å55.19 Å
Translation5.93 Å55.19 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ADB
Resolution: 1.7→68.78 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1622 8907 5.02 %
Rwork0.1455 168461 -
obs0.1463 177368 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.48 Å2 / Biso mean: 22.79 Å2 / Biso min: 8.33 Å2
Refinement stepCycle: final / Resolution: 1.7→68.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11324 0 23 1609 12956
Biso mean--36.24 33.74 -
Num. residues----1564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.720.18512890.1527541795
1.72-1.740.18662610.146542496
1.74-1.760.17962960.1421551197
1.76-1.780.17713100.144554698
1.78-1.810.16673160.1405553799
1.81-1.830.1673120.1431561599
1.83-1.860.16583060.1392560499
1.86-1.890.173170.1382565399
1.89-1.910.17442800.1407556599
1.91-1.950.17342840.1425563499
1.95-1.980.17713070.14485651100
1.98-2.020.18123160.14595561100
2.02-2.050.16683170.14695624100
2.05-2.10.16543000.14455630100
2.1-2.140.17312750.1435631100
2.14-2.190.15372950.145660100
2.19-2.250.17222820.1455678100
2.25-2.310.18063240.14355613100
2.31-2.380.1783080.14665602100
2.38-2.450.17952970.15475652100
2.45-2.540.17312940.15075667100
2.54-2.640.16882840.1525670100
2.64-2.760.17773000.1595659100
2.76-2.910.16212820.15195646100
2.91-3.090.15472940.14975649100
3.09-3.330.15913070.14665648100
3.33-3.660.14383140.14255642100
3.66-4.190.14082870.13075687100
4.19-5.280.14272470.1325720100
5.28-68.780.15593060.1559566599
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)
10.241-0.1931-0.04571.3779-0.07190.4962-0.1096-0.05050.12420.1020.0416-0.2617-0.22230.18370.07060.2259-0.0662-0.05460.2001-0.00020.174533.051945.659433.7355
20.84180.72210.13851.6912-0.51050.5947-0.0313-0.1752-0.01720.3095-0.00030.1524-0.20180.04740.04220.2040.03390.03720.20530.01820.144912.950531.576145.4388
30.4341-0.17120.20421.2353-0.21621.5249-0.0161-0.0151-0.0507-0.07720.06610.227-0.023-0.0674-0.04210.10990.0056-0.01990.10720.02490.14947.946432.833322.9827
41.0187-0.86540.32461.2753-0.67160.77280.11510.17-0.0378-0.331-0.09110.08860.05940.1785-0.02420.2446-0.0016-0.01960.1837-0.00310.133517.636435.1598.5734
50.2719-0.14610.0850.9099-0.28370.8714-0.0519-0.0241-0.0045-0.04440.06230.1805-0.1339-0.0677-0.00960.14260.0075-0.02070.12550.01250.15877.819539.469322.8436
60.52010.49550.23751.1256-0.56521.0675-0.27160.33980.3722-0.26570.15460.2286-0.4704-0.13710.02380.4046-0.0747-0.09580.17410.05340.20818.50561.214820.4796
70.56220.31610.22740.9041-0.11650.8751-0.16210.07190.0875-0.01350.0463-0.2181-0.28860.25510.09520.3248-0.1011-0.06480.18110.02560.190827.900558.398825.2088
80.9648-0.11430.06851.089-0.010.5921-0.0583-0.136-0.13460.11950.20810.53890.017-0.3719-0.04590.14710.0280.07250.22840.08230.3019-0.272823.922737.8272
90.3497-0.16780.13090.5056-0.26410.4977-0.0889-0.2013-0.07280.28950.08750.0543-0.1818-0.06310.0130.17230.04020.04780.18880.03120.112319.175628.312845.9631
101.4075-0.29420.46361.8407-0.39621.54-0.0722-0.0123-0.01390.1447-0.0261-0.3318-0.06490.21160.04650.1219-0.018-0.00770.18550.01020.173737.304227.854533.1166
110.6655-0.27950.25681.5573-0.08030.9393-0.00850.1083-0.0706-0.155-0.02410.10950.00740.0240.03460.14750.00440.00620.1577-0.0030.133925.736319.139319.3623
121.5087-0.62260.27531.5014-0.00270.64930.0630.2103-0.1948-0.2729-0.07220.04730.03220.10920.02430.20180.00370.00140.1728-0.03240.193320.571611.983917.645
131.08880.12540.02921.5274-0.6151.3827-0.04840.1496-0.2347-0.2375-0.0162-0.01030.2140.07710.05260.14490.03790.04060.184-0.00950.167931.90779.410522.6522
140.19630.1067-0.05940.4132-0.52221.3662-0.0485-0.0224-0.1495-0.0096-0.0177-0.05490.06060.18120.0520.1390.02590.03040.1980.03120.181733.016414.809434.297
150.4984-0.05270.17470.7498-0.00450.5818-0.0653-0.0579-0.02920.0550.0266-0.0812-0.15460.09710.04680.1319-0.00380.00680.18230.01370.126530.201328.2933.8959
161.68480.721-0.0290.9009-0.10570.5083-0.3713-0.0753-1.04380.00060.2036-0.21320.46350.10460.00880.18780.09060.11940.17830.12480.456321.86921.704144.117
170.1959-0.0106-0.47360.83780.6121.573-0.2216-0.0366-0.3648-0.02830.0270.32590.0561-0.44090.030.13650.00660.1120.26560.07970.27157.80868.08243.4565
180.55520.0562-0.24050.2161-0.07881.0997-0.237-0.2706-0.71080.16490.14220.2290.3018-0.10010.05380.12690.00850.24290.21620.20120.33514.86915.591147.7206
191.0664-0.10780.06881.0916-0.52311.05620.05550.3334-0.2836-0.5158-0.0421-0.17510.17410.0864-0.02610.23890.0240.02750.2216-0.07370.191412.013-21.9047-15.8154
200.4945-0.1484-0.09421.21040.14280.57480.0474-0.0211-0.14850.05330.04260.15470.115-0.0828-0.08420.1224-0.0145-0.02360.15130.03210.1593-4.1046-22.50245.0266
210.7625-0.22490.13111.2348-0.47050.84280.03-0.0069-0.05350.2208-0.026-0.20650.00170.1076-0.02480.1712-0.0044-0.06820.14430.01310.168418.9068-18.803517.4572
220.72690.04330.09630.8145-0.08080.42280.0484-0.0829-0.1430.11940.0437-0.01460.0703-0.0411-0.08660.1729-0.0017-0.03570.15140.030.14134.6495-23.529716.1208
230.60910.00240.20051.48440.4150.90810.10070.0205-0.24640.07940.1358-0.20680.28780.105-0.17730.17860.0197-0.0850.1435-0.02060.22548.5777-35.92894.3144
240.134-0.00680.08441.3722-0.27811.1538-0.0284-0.2497-0.05650.41270.13950.4152-0.0895-0.297-0.09580.2220.04530.08520.24560.04440.2067-10.0516-6.79119.4539
250.7633-0.2191-0.01160.7865-0.01850.64720.0630.0515-0.0533-0.09180.04250.1555-0.0027-0.1282-0.08770.1001-0.0049-0.00910.14620.02340.1166-4.4508-10.7985-5.9481
260.8031-0.0047-0.05961.0601-0.43081.1790.03390.03410.08640.089-0.0232-0.1386-0.14780.067-0.00830.119-0.01790.00360.12590.00660.13716.0294.4580.6295
271.15990.0103-0.31090.6433-0.13310.85250.12590.05590.2196-0.01440.03320.0602-0.2136-0.1226-0.14070.13680.02530.03920.14550.03360.1418-3.97714.4008-3.2433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 62 )A7 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 85 )A63 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 143 )A86 - 143
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 180 )A144 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 306 )A181 - 306
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 346 )A307 - 346
7X-RAY DIFFRACTION7chain 'A' and (resid 347 through 397 )A347 - 397
8X-RAY DIFFRACTION8chain 'B' and (resid 7 through 29 )B7 - 29
9X-RAY DIFFRACTION9chain 'B' and (resid 30 through 85 )B30 - 85
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 112 )B86 - 112
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 143 )B113 - 143
12X-RAY DIFFRACTION12chain 'B' and (resid 144 through 180 )B144 - 180
13X-RAY DIFFRACTION13chain 'B' and (resid 181 through 224 )B181 - 224
14X-RAY DIFFRACTION14chain 'B' and (resid 225 through 251 )B225 - 251
15X-RAY DIFFRACTION15chain 'B' and (resid 252 through 304 )B252 - 304
16X-RAY DIFFRACTION16chain 'B' and (resid 305 through 346 )B305 - 346
17X-RAY DIFFRACTION17chain 'B' and (resid 347 through 365 )B347 - 365
18X-RAY DIFFRACTION18chain 'B' and (resid 366 through 397 )B366 - 397
19X-RAY DIFFRACTION19chain 'C' and (resid 7 through 29 )C7 - 29
20X-RAY DIFFRACTION20chain 'C' and (resid 30 through 112 )C30 - 112
21X-RAY DIFFRACTION21chain 'C' and (resid 113 through 224 )C113 - 224
22X-RAY DIFFRACTION22chain 'C' and (resid 225 through 272 )C225 - 272
23X-RAY DIFFRACTION23chain 'C' and (resid 273 through 397 )C273 - 397
24X-RAY DIFFRACTION24chain 'D' and (resid 7 through 29 )D7 - 29
25X-RAY DIFFRACTION25chain 'D' and (resid 30 through 112 )D30 - 112
26X-RAY DIFFRACTION26chain 'D' and (resid 113 through 224 )D113 - 224
27X-RAY DIFFRACTION27chain 'D' and (resid 225 through 397 )D225 - 397

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