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- PDB-7kz6: Crystal structure of KabA from Bacillus cereus UW85 with bound co... -

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Basic information

Entry
Database: PDB / ID: 7kz6
TitleCrystal structure of KabA from Bacillus cereus UW85 with bound cofactor PMP
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / Kanosamine / Biosynthesis / Aminotransferase / KabA
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
: / NTD biosynthesis operon protein NtdA, N-terminal domain / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / KabA
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPrasertanan, T. / Palmer, D.R.J. / Sanders, D.A.R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Snapshots along the catalytic path of KabA, a PLP-dependent aminotransferase required for kanosamine biosynthesis in Bacillus cereus UW85.
Authors: Prasertanan, T. / Palmer, D.R.J. / Sanders, D.A.R.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 2023Group: 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: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
B: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
C: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
D: Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,66636
Polymers203,9364
Non-polymers2,73132
Water21,8701214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The data suggest that KabA is of high purity and is a tetramer in solution using size exclusion chromatography to estimate molecular weight corresponded to the observed ...Evidence: gel filtration, The data suggest that KabA is of high purity and is a tetramer in solution using size exclusion chromatography to estimate molecular weight corresponded to the observed molecular weight based on Native (non-denaturing) gel electrophoresis analysis.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.530, 66.640, 112.220
Angle α, β, γ (deg.)77.420, 81.060, 88.340
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme / KabA


Mass: 50983.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: kabA, GE376_30835 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C0JRF5, aspartate transaminase
#2: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1214 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 1.65→46.88 Å / Num. obs: 213145 / % possible obs: 95.31 % / Redundancy: 2.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.03571 / Rpim(I) all: 0.02951 / Rrim(I) all: 0.04656 / Net I/σ(I): 12.87
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.3399 / Num. unique obs: 21216 / CC1/2: 0.801 / CC star: 0.943 / Rpim(I) all: 0.2905 / Rrim(I) all: 0.4488 / % possible all: 94.74

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Processing

Software
NameVersionClassification
PHENIXdev_2398refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
AutoProcessdata reduction
AutoProcessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KZ3

7kz3


Resolution: 1.65→46.876 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 10658 5 %
Rwork0.1677 202478 -
obs0.1694 213136 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.82 Å2 / Biso mean: 34.9603 Å2 / Biso min: 11.63 Å2
Refinement stepCycle: final / Resolution: 1.65→46.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14127 0 176 1216 15519
Biso mean--37.19 37.8 -
Num. residues----1753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01314665
X-RAY DIFFRACTIONf_angle_d1.27519736
X-RAY DIFFRACTIONf_chiral_restr0.0762213
X-RAY DIFFRACTIONf_plane_restr0.0092525
X-RAY DIFFRACTIONf_dihedral_angle_d16.3228990
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66880.27963530.2348669794
1.6688-1.68840.26863490.2322664195
1.6884-1.7090.2543590.2191681795
1.709-1.73060.24613510.212667695
1.7306-1.75340.2533580.2063680395
1.7534-1.77740.24933480.2014660995
1.7774-1.80280.24773580.2049680595
1.8028-1.82970.26433510.2144666295
1.8297-1.85830.25513570.2066677495
1.8583-1.88880.23583530.1963670295
1.8888-1.92130.23453540.1907672695
1.9213-1.95630.21253600.1853685495
1.9563-1.99390.21633490.1793662195
1.9939-2.03460.2143590.1714681896
2.0346-2.07880.20443580.1686681596
2.0788-2.12720.19873530.1689670595
2.1272-2.18040.22013540.1684672695
2.1804-2.23930.22983560.1721675195
2.2393-2.30520.20493580.1685681496
2.3052-2.37960.21623600.1686684396
2.3796-2.46470.23560.1661675695
2.4647-2.56340.2113560.1679676896
2.5634-2.680.20473570.1701678496
2.68-2.82130.21723570.1766678796
2.8213-2.9980.19943550.1754674595
2.998-3.22950.20693510.1737666895
3.2295-3.55440.17893570.1621677195
3.5544-4.06840.16883540.1443673595
4.0684-5.12480.1643590.1388681296
5.1248-46.8760.18653580.1572679396
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6755-0.08840.81472.816-1.30171.32110.12480.18230.4693-0.1558-0.06720.1877-0.6211-0.25820.00170.4220.0574-0.01070.20330.01350.2793-2.175413.6067-16.0539
20.4679-0.3319-0.08961.06180.24041.35730.04090.10470.0178-0.2227-0.11210.0963-0.1703-0.1040.00580.1632-0.0434-0.01870.1962-0.00060.20942.9896-3.3842-8.9213
33.0388-0.18240.84352.24590.39123.1558-0.0952-0.10150.11390.19-0.07230.1546-0.1864-0.28250.09110.1335-0.05770.01120.2167-0.00690.20171.527-1.558115.0034
41.5734-0.03570.55131.16970.74932.9869-0.0667-0.19350.20680.18010.0532-0.028-0.3740.10280.06460.2636-0.0678-0.03630.2395-0.03940.28857.39286.880314.7875
50.7669-0.40470.13740.88260.05611.35470.0113-0.01740.078-0.1036-0.0414-0.0122-0.1730.13310.04280.1258-0.0784-0.00040.15560.00320.17529.3405-3.213-3.1226
62.92-0.0499-1.22870.1558-0.38131.85080.4512-0.04070.4241-0.2052-0.26040.4654-0.5911-0.2624-0.14990.18060.03050.01210.25-0.10480.4131-15.42888.09242.5588
72.051-0.3091-0.34821.53130.14050.8247-0.0754-0.2889-0.0990.1628-0.04270.28010.0689-0.4242-0.19340.1056-0.05470.02860.3054-0.05770.3343-15.3195-4.93967.8936
81.70880.86440.44152.4818-0.08620.4502-0.31590.2936-0.5216-0.37830.1343-0.18250.59020.2354-0.00930.57770.0470.10020.2822-0.0420.359818.1406-45.6977-20.6764
90.5644-0.15090.42231.2590.14341.66530.03070.114-0.079-0.2539-0.13950.10060.32770.24090.12580.23930.0070.0160.24890.00830.212712.8501-25.1431-15.9819
101.0644-0.1178-0.15211.40210.70311.9246-0.0499-0.2381-0.14170.39140.0357-0.01820.64830.3972-0.04140.36180.06130.03270.26370.06380.219120.9294-31.4997.8745
110.2852-0.392-0.19482.0686-0.1171.9804-0.1132-0.1365-0.02990.282-0.02770.42790.2078-0.27230.05950.2416-0.08220.06180.2604-0.00030.32772.5998-22.968.3829
122.0858-0.05680.52141.5690.45042.4632-0.01720.0945-0.01460.03790.1083-0.34040.61690.95080.00220.16150.19870.04510.48450.01620.229334.7415-30.1468-7.7624
131.4386-0.28840.49533.3561-0.26241.8155-0.1798-0.2702-0.20590.48450.2564-0.21830.36960.4836-0.05160.30270.1175-0.01320.52920.04680.262825.3773-19.4116-37.3145
140.7292-0.6907-0.27110.84880.67360.5724-0.1657-0.3092-0.21610.29290.1418-0.12530.36350.0924-0.04040.40330.01120.03570.2910.06920.29543.062-18.9866-39.5374
154.9311-1.6279-1.59692.04670.49821.8568-0.05150.07560.5246-0.03260.0019-0.1093-0.50020.06890.05580.3043-0.1308-0.04340.2343-0.01530.195510.04941.7125-44.3432
160.9424-0.0316-0.00071.7130.4682.4117-0.00390.12110.0032-0.3565-0.0527-0.1061-0.20030.3690.05650.2513-0.08310.02670.20350.03940.212715.5851-7.3207-68.2116
170.7201-0.5584-0.06471.3540.01031.9073-0.0239-0.07360.1272-0.10850.0144-0.0395-0.43340.12930.01770.2541-0.0997-0.02020.15720.00610.18749.13130.8055-55.9427
180.9517-0.27340.00741.2770.2041.9449-0.0789-0.0034-0.2886-0.0975-0.00260.04060.52820.2819-0.02190.28350.00960.05870.14650.03580.262312.0173-27.1877-58.2536
192.64191.02960.24551.10640.0730.04720.0843-0.36760.1640.2023-0.37210.6735-0.1398-0.63820.12910.29850.0959-0.0020.6437-0.13460.4091-31.57635.2298-35.0249
201.1143-0.7863-0.40511.47820.46061.5372-0.1458-0.31290.13620.0181-0.06480.0342-0.5426-0.28240.00910.35890.069-0.03320.2839-0.02480.2104-8.89014.7406-34.2834
211.60670.0502-0.59421.24970.35771.95710.04170.34850.0304-0.3333-0.11840.2279-0.4431-0.6725-0.1250.33270.1129-0.1070.3983-0.05340.2665-16.92844.9927-61.7304
222.56-0.3221-0.36540.91160.46021.9292-0.05980.1592-0.5187-0.1236-0.12780.16050.1448-0.23160.11830.2647-0.0632-0.03870.2565-0.05150.3099-9.0702-11.2222-63.8761
231.3929-0.17-0.40891.7893-0.05372.18340.11220.00210.3568-0.1452-0.08990.0383-0.9576-0.5676-0.14410.58620.2195-0.0510.2554-0.04430.3077-15.504621.1828-47.7441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 47 )A6 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 158 )A48 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 185 )A159 - 185
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 229 )A186 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 334 )A230 - 334
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 358 )A335 - 358
7X-RAY DIFFRACTION7chain 'A' and (resid 359 through 443 )A359 - 443
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 67 )B6 - 67
9X-RAY DIFFRACTION9chain 'B' and (resid 68 through 121 )B68 - 121
10X-RAY DIFFRACTION10chain 'B' and (resid 122 through 262 )B122 - 262
11X-RAY DIFFRACTION11chain 'B' and (resid 263 through 303 )B263 - 303
12X-RAY DIFFRACTION12chain 'B' and (resid 304 through 443 )B304 - 443
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 67 )C6 - 67
14X-RAY DIFFRACTION14chain 'C' and (resid 68 through 101 )C68 - 101
15X-RAY DIFFRACTION15chain 'C' and (resid 102 through 121 )C102 - 121
16X-RAY DIFFRACTION16chain 'C' and (resid 122 through 229 )C122 - 229
17X-RAY DIFFRACTION17chain 'C' and (resid 230 through 303 )C230 - 303
18X-RAY DIFFRACTION18chain 'C' and (resid 304 through 443 )C304 - 443
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 67 )D5 - 67
20X-RAY DIFFRACTION20chain 'D' and (resid 68 through 101 )D68 - 101
21X-RAY DIFFRACTION21chain 'D' and (resid 102 through 262 )D102 - 262
22X-RAY DIFFRACTION22chain 'D' and (resid 263 through 303 )D263 - 303
23X-RAY DIFFRACTION23chain 'D' and (resid 304 through 443 )D304 - 443

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