[English] 日本語
Yorodumi
- PDB-7kz3: Crystal structure of KabA from Bacillus cereus UW85 in complex wi... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 1436 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more