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- PDB-7kz3: Crystal structure of KabA from Bacillus cereus UW85 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7kz3
TitleCrystal structure of KabA from Bacillus cereus UW85 in complex with the internal aldimine
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / Kanosamine / Biosynthesis / Aminotransferase / KabA
Function / homologyDegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / polysaccharide biosynthetic process / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / pyridoxal phosphate binding / Aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 9, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)209,17775
Polymers204,8484
Non-polymers4,32971
Water25,8701436
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)66.460, 66.680, 111.830
Angle α, β, γ (deg.)81.080, 77.410, 88.050
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: 51212.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: LLP is a modified residue between K and PLP as internal aldimine.
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: kabA, GE376_30835 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C0JRF5, aspartate transaminase
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 69 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1436 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
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: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.814 Å / Relative weight: 1
ReflectionResolution: 1.55→46.2441 Å / Num. obs: 251426 / % possible obs: 93.56 % / Redundancy: 2.2 % / Biso Wilson estimate: 17.3 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03018 / Rpim(I) all: 0.02732 / Rrim(I) all: 0.04084 / Net I/σ(I): 16.29
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.2868 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 25082 / CC1/2: 0.845 / CC star: 0.957 / Rpim(I) all: 0.2606 / % possible all: 93.68

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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: 4K2B

4k2b


Resolution: 1.55→46.2441 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1809 12569 5 %
Rwork0.1496 238844 -
obs0.1512 251413 93.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.17 Å2 / Biso mean: 25.3163 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.55→46.2441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14208 0 278 1436 15922
Biso mean--36.83 34.39 -
Num. residues----1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01914791
X-RAY DIFFRACTIONf_angle_d1.6919828
X-RAY DIFFRACTIONf_chiral_restr0.1242221
X-RAY DIFFRACTIONf_plane_restr0.0112525
X-RAY DIFFRACTIONf_dihedral_angle_d16.2859031
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.56760.25184170.2126792394
1.5676-1.58610.24114220.2022800693
1.5861-1.60540.22994150.1995790094
1.6054-1.62570.22254250.1918807393
1.6257-1.64710.21514180.1809792794
1.6471-1.66970.2094240.1775806894
1.6697-1.69350.21144200.1802797294
1.6935-1.71880.23524170.1802792994
1.7188-1.74570.19984220.1717801294
1.7457-1.77430.20974170.1681791894
1.7743-1.80490.21584220.1672801794
1.8049-1.83770.20714170.1593793994
1.8377-1.87310.20674170.1561792193
1.8731-1.91130.18044190.1489795493
1.9113-1.95290.19234190.1498795893
1.9529-1.99830.17734110.1485781693
1.9983-2.04830.17924130.1504783492
2.0483-2.10360.18084100.1487780091
2.1036-2.16550.18814130.1465784192
2.1655-2.23540.1814050.1413770891
2.2354-2.31530.16774100.1385777291
2.3153-2.4080.17364100.142780392
2.408-2.51760.19384140.149786792
2.5176-2.65030.17094160.1511790692
2.6503-2.81640.19024180.1547794194
2.8164-3.03380.18944240.152807795
3.0338-3.3390.16824320.1467819596
3.339-3.8220.15494330.1339822597
3.822-4.81450.15154380.1256832198
4.8145-46.24410.17974310.1539822197
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)
12.3487-0.0979-0.76611.16091.13411.52330.21830.1475-0.4728-0.1574-0.07280.0270.43240.21280.06470.30290.0469-0.02350.1871-0.04010.24951.2384-13.5585-15.8576
20.9675-0.2934-0.0780.76480.23730.36210.12330.159-0.0934-0.2546-0.1011-0.0934-0.01030.0676-0.01490.28570.02160.04310.2417-0.00080.16136.61472.6449-18.753
31.3185-1.83430.19196.2275-1.28790.88390.07830.0059-0.1852-0.1228-0.11240.6025-0.0608-0.1561-0.00330.1503-0.0294-0.04060.2078-0.04110.1754-16.24954.21-11.256
41.02710.12970.33450.71910.16821.1533-0.0229-0.2472-0.14860.1090.01420.03850.1399-0.09250.04160.1125-0.03950.02680.17050.03260.1494-7.8079-1.475212.6823
51.0539-0.375-0.04290.51150.01250.67310.0277-0.0065-0.1059-0.0714-0.030.07630.0512-0.09280.00690.1046-0.03530.00380.0972-0.00770.1171-9.51263.0085-3.046
63.54730.01341.40931.07680.47491.79920.2704-0.2203-0.53210.0086-0.0172-0.08920.41050.0986-0.17360.15710.0258-0.01090.16420.03280.211515.1477-8.1382.556
71.0487-0.3588-0.2280.8770.32950.6507-0.053-0.14880.0310.0270.0483-0.15940.00210.20790.02150.0849-0.0203-0.00060.18080.00450.152914.92234.76227.9033
82.78290.35650.35221.80731.03342.0566-0.0075-0.1731-0.18050.2451-0.0397-0.39570.15980.36470.03580.14580.0114-0.01240.29910.05130.232832.0839-3.7672-38.2254
91.1947-0.30740.17251.0777-0.2790.7555-0.1326-0.22550.07980.15780.0351-0.15860.00650.15720.09380.20630.0158-0.0050.247-0.01440.139615.7588-1.4944-35.9307
100.8247-0.06050.17710.79380.10840.96690.00030.1749-0.0136-0.1357-0.0227-0.08420.12560.2644-0.01150.13880.01310.040.20170.02380.114916.4678-7.6975-62.9971
112.7659-0.2522-0.10870.28080.04441.3988-0.06530.20610.3899-0.1198-0.0472-0.0525-0.22770.05640.05130.1901-0.048-00.16850.04270.198.60510.8106-63.7969
120.7566-0.24470.24571.49040.02361.09030.0097-0.0123-0.17990.0251-0.0020.03010.33630.1982-0.03030.19310.05510.04740.15640.02570.171714.8397-21.4533-47.322
131.08080.6373-0.01992.23170.48140.5811-0.23430.2040.3884-0.37260.06190.0623-0.3392-0.04470.12530.3975-0.0005-0.06410.19620.02030.3108-17.7145.7285-20.4825
142.8061-1.48350.67791.3243-0.49880.61850.12680.23420.0022-0.2523-0.18240.09270.0121-0.08320.05050.27010.058-0.0120.2188-0.02820.1605-18.478123.2665-21.3323
152.0426-2.5924-0.16465.81550.92411.1829-0.1236-0.02680.1910.12980.0621-0.5716-0.12580.17880.0310.173-0.06120.0010.1652-0.00670.2381-2.638428.4067-6.393
161.12730.01310.15181.0471-0.29770.6517-0.076-0.30430.18990.20570.03780.0434-0.3072-0.1791-0.05310.24060.0598-0.020.2095-0.07160.176-20.725831.48367.8702
170.4264-0.30380.42642.7616-0.81591.7084-0.0731-0.14420.11910.0962-0.0354-0.3235-0.06620.09570.06020.1375-0.031-0.01710.1532-0.02890.1726-2.64222.90218.4812
181.3977-0.29210.14830.7015-0.23191.0432-0.0513-0.08490.0059-0.00960.04650.2122-0.2222-0.3668-0.04860.19730.0745-0.02170.2142-0.04090.2219-34.61130.3699-7.8126
191.58010.2078-0.96012.84590.53612.2378-0.0414-0.14320.11630.1650.15570.4129-0.2721-0.44390.06930.20030.04920.03610.26970.01080.236-27.546916.1541-39.3149
202.73260.5357-0.39634.4441.0943.30120.0043-0.22170.21280.258-0.00090.4117-0.10370.143-0.07270.28290.06350.00630.3018-0.03580.2261-22.914924.3155-32.4743
211.1354-1.16410.06483.1226-1.19050.8997-0.1434-0.22160.140.18330.16840.0211-0.11180.1032-0.030.23820.0087-0.03270.2274-0.05070.1703-3.618718.8993-39.2078
223.37-1.22450.74861.1744-0.25751.2702-0.14870.0074-0.35840.07130.08910.19870.09670.0330.00880.1936-0.0220.03510.1510.02830.1822-10.5688-1.898-43.8199
230.6429-0.1061-0.04070.542-0.16941.42460.02410.0973-0.0036-0.1006-0.06050.0716-0.0141-0.11580.03670.1604-0.0245-0.02090.1289-0.01430.1725-15.98346.5832-67.8656
240.6346-0.3595-0.08230.86310.16860.5308-0.0213-0.036-0.0219-0.01530.00730.05980.0412-0.05650.01610.1124-0.03040.00810.09650.00870.1198-11.344.7647-52.1997
251.3263-0.1458-0.55463.7507-1.55361.8114-0.0190.11430.2164-0.25430.19960.4201-0.1011-0.2399-0.1580.2188-0.0016-0.050.13250.02290.2373-20.25130.9101-59.6605
260.9657-0.05160.11481.78160.17161.03180.03490.12030.187-0.27680.0003-0.105-0.13510.1032-0.03020.1934-0.0298-0.00640.11170.03190.2103-8.289928.6268-62.9611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )A5 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 101 )A48 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 121 )A102 - 121
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 229 )A122 - 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 5 through 47 )B5 - 47
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 121 )B48 - 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 5 through 67 )C5 - 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 262 )C122 - 262
17X-RAY DIFFRACTION17chain 'C' and (resid 263 through 303 )C263 - 303
18X-RAY DIFFRACTION18chain 'C' and (resid 304 through 443 )C304 - 443
19X-RAY DIFFRACTION19chain 'D' and (resid 5 through 47 )D5 - 47
20X-RAY DIFFRACTION20chain 'D' and (resid 48 through 67 )D48 - 67
21X-RAY DIFFRACTION21chain 'D' and (resid 68 through 101 )D68 - 101
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 121 )D102 - 121
23X-RAY DIFFRACTION23chain 'D' and (resid 122 through 229 )D122 - 229
24X-RAY DIFFRACTION24chain 'D' and (resid 230 through 334 )D230 - 334
25X-RAY DIFFRACTION25chain 'D' and (resid 335 through 366 )D335 - 366
26X-RAY DIFFRACTION26chain 'D' and (resid 367 through 443 )D367 - 443

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