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- PDB-7kz5: Crystal structure of KabA from Bacillus cereus UW85 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7kz5
TitleCrystal structure of KabA from Bacillus cereus UW85 in complex with the plp external aldimine adduct with kanosamine-6-phosphate
ComponentsAminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / Kanosamine / Biosynthesis / Aminotransferase / KabA
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
: / NTD biosynthesis operon protein NtdA, N-terminal domain / DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)209,10061
Polymers203,9364
Non-polymers5,16557
Water21,6721203
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)66.670, 66.600, 111.780
Angle α, β, γ (deg.)77.350, 81.060, 87.910
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: Sugar
ChemComp-O1G / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco pyranose / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco se / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-D-glucose / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 488.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H22N2O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1203 / 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: 47.57 %
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: 1.6→46.748 Å / Num. obs: 227037 / % possible obs: 92.8 % / Redundancy: 2.2 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04613 / Rpim(I) all: 0.04186 / Rrim(I) all: 0.06249 / Net I/σ(I): 10.49
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3387 / Num. unique obs: 22494 / CC1/2: 0.784 / CC star: 0.937 / Rpim(I) all: 0.3128 / Rrim(I) all: 0.4623 / % possible all: 92.03

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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: 1.6→46.748 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 11352 5 %
Rwork0.1747 215677 -
obs0.1768 227029 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.4 Å2 / Biso mean: 24.7165 Å2 / Biso min: 8.8 Å2
Refinement stepCycle: final / Resolution: 1.6→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14148 0 330 1204 15682
Biso mean--28.59 32.8 -
Num. residues----1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214841
X-RAY DIFFRACTIONf_angle_d1.61619942
X-RAY DIFFRACTIONf_chiral_restr0.1142245
X-RAY DIFFRACTIONf_plane_restr0.0112536
X-RAY DIFFRACTIONf_dihedral_angle_d15.0939050
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.61820.28353550.2411675787
1.6182-1.63720.29683840.2394729795
1.6372-1.65720.27083850.2286731695
1.6572-1.67820.26773880.2196735895
1.6782-1.70030.25613850.2116731595
1.7003-1.72360.25843850.2066732294
1.7236-1.74820.24263890.1938739995
1.7482-1.77430.24113830.196726494
1.7743-1.8020.25853880.2047737194
1.802-1.83150.25373810.196723595
1.8315-1.86310.24163850.1939732894
1.8631-1.8970.2433800.1921721594
1.897-1.93350.24083700.1912702791
1.9335-1.9730.23353790.1819721193
1.973-2.01590.2163830.1746726293
2.0159-2.06280.21263690.1679701092
2.0628-2.11430.20083660.1685696290
2.1143-2.17150.20643740.1677710192
2.1715-2.23540.23433720.1701707891
2.2354-2.30760.2043600.1728683388
2.3076-2.390.21233720.168707391
2.39-2.48570.21643720.1781706692
2.4857-2.59880.21073730.172709591
2.5988-2.73580.21973730.1752708492
2.7358-2.90720.2333810.1784723093
2.9072-3.13160.21413770.1713716793
3.1316-3.44670.20253830.1713727394
3.4467-3.94520.193820.1558725093
3.9452-4.96970.17473860.1476734795
4.9697-46.7480.21493920.178743196
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)
12.34550.89480.45492.725-0.96722.34440.14880.16740.3633-0.2155-0.12730.1268-0.4314-0.3370.01660.25620.04610.0090.17360.02130.2332-3.663114.1766-17.5663
26.80871.88581.13894.7639-0.24382.6849-0.0310.08820.5111-0.4149-0.07670.22550.1812-0.09760.14550.26720.0305-0.04160.2301-0.00040.1685-11.80729.6147-24.5638
32.4709-1.1806-0.92091.1512-0.09830.690.17780.34670.0232-0.2367-0.16890.12350.133-0.2421-0.0340.24540.0082-0.04650.2408-0.0510.1438-7.0713-9.9447-17.7818
40.8094-0.22920.01150.6733-0.01041.2683-0.0374-0.17010.14260.07540.005-0.0711-0.10910.04870.03150.121-0.0411-0.0140.1554-0.02440.17596.22480.97225.0884
51.1872-0.3255-0.00370.5875-0.08880.5955-0.0159-0.15430.05420.02450.02580.0936-0.0272-0.07950.00750.0978-0.0378-0.00360.1203-0.02070.1393-6.9164-2.01280.8927
60.74680.3126-0.27521.604-0.30090.2832-0.24820.291-0.331-0.28830.054-0.00170.2674-0.13690.10790.3081-0.00240.05940.1407-0.04040.239315.3812-45.2879-22.1434
71.4721-0.7996-0.54061.00930.50271.04180.03940.33510.0508-0.2544-0.1597-0.009-0.00530.02860.01370.23180.0587-0.00050.18680.00690.139515.974-22.8915-23.1409
81.1919-0.00010.03790.9910.17051.1131-0.0176-0.2436-0.07990.20570.00810.00940.26510.1292-0.01310.21790.0060.02140.17510.0280.141217.0432-30.53976.5614
90.7581-0.4813-0.24831.24170.29521.2531-0.0535-0.0661-0.0610.10840.01320.20260.1464-0.11160.04330.1578-0.0410.01650.13870.01090.16126.6106-26.01182.1248
101.3707-0.301-0.0450.85060.22191.1279-0.0196-0.06840.03750.01210.0332-0.20280.20620.366-0.04030.14480.05470.01870.18430.01570.164232.2761-29.7439-9.6854
110.62390.12570.20412.1698-0.27712.1504-0.0618-0.1394-0.090.21630.0807-0.35240.15240.2088-0.00590.1850.0351-0.04550.2450.00810.23323.6151-18.4748-38.7698
121.0764-0.58440.27710.91570.16850.6551-0.1441-0.22880.00550.12120.1217-0.0473-0.0097-0.03710.01720.17360.00590.00860.18320.01170.13093.3154-11.0924-42.4136
130.9655-0.30080.03641.1001-0.06771.32340.01530.08310.0325-0.1827-0.0482-0.1476-0.0260.10110.02520.1366-0.03990.01890.10830.00510.155313.0365-6.7244-66.3064
140.6781-0.42670.01211.29430.02720.66230.00960.0184-0.0929-0.11080.0046-0.01870.08950.03090.00850.0939-0.04370.01610.08690.00220.11798.7561-18.7492-59.557
152.85780.60490.24010.7633-0.41061.28170.0446-0.19130.16260.0412-0.10380.4083-0.1987-0.27490.10280.15270.01440.0170.2992-0.05350.299-34.96674.4053-40.1747
161.1556-0.2889-0.23021.05610.48850.8168-0.1226-0.2282-0.06360.21970.01350.16090.0185-0.19120.09310.19750.01540.02490.23010.01320.1583-18.30531.7311-37.7098
171.1326-0.1731-0.3951.1857-0.07331.03610.06450.270.0655-0.2734-0.050.177-0.1426-0.3265-0.03290.20790.0386-0.05080.2477-0.00890.1713-19.08717.9548-64.9282
181.4928-0.3441-0.16020.41630.28490.9212-0.01550.1483-0.312-0.1688-0.05320.1640.0477-0.0690.01580.1914-0.0454-0.0340.2093-0.05010.1935-11.3985-10.2841-65.477
190.8492-0.2803-0.40441.38380.29471.06750.09730.01840.2319-0.0907-0.0286-0.0449-0.3685-0.2389-0.03120.20920.0657-0.00820.13440.00160.2012-17.507521.3953-48.9914
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 67 )A48 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 101 )A68 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 262 )A102 - 262
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 443 )A263 - 443
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 67 )B5 - 67
7X-RAY DIFFRACTION7chain 'B' and (resid 68 through 101 )B68 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 102 through 229 )B102 - 229
9X-RAY DIFFRACTION9chain 'B' and (resid 230 through 303 )B230 - 303
10X-RAY DIFFRACTION10chain 'B' and (resid 304 through 443 )B304 - 443
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 67 )C5 - 67
12X-RAY DIFFRACTION12chain 'C' and (resid 68 through 120 )C68 - 120
13X-RAY DIFFRACTION13chain 'C' and (resid 121 through 262 )C121 - 262
14X-RAY DIFFRACTION14chain 'C' and (resid 263 through 443 )C263 - 443
15X-RAY DIFFRACTION15chain 'D' and (resid 5 through 47 )D5 - 47
16X-RAY DIFFRACTION16chain 'D' and (resid 48 through 121 )D48 - 121
17X-RAY DIFFRACTION17chain 'D' and (resid 122 through 262 )D122 - 262
18X-RAY DIFFRACTION18chain 'D' and (resid 263 through 303 )D263 - 303
19X-RAY DIFFRACTION19chain 'D' and (resid 304 through 443 )D304 - 443

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