[English] 日本語
Yorodumi
- PDB-3n5m: Crystals structure of a Bacillus anthracis aminotransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3n5m
TitleCrystals structure of a Bacillus anthracis aminotransferase
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Bacillus anthracis / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / DiLeo, R. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystals structure of a Bacillus anthracis aminotransferase
Authors: Anderson, S.M. / Wawrzak, Z. / DiLeo, R. / Onopriyenko, O. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references / Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
C: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
D: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,95520
Polymers204,9034
Non-polymers1,05216
Water18,7001038
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31450 Å2
ΔGint-468 kcal/mol
Surface area53120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.414, 176.176, 80.059
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 5 - 449 / Label seq-ID: 8 - 452

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 5:449 )AA
2chain B and (resseq 5:449 )BB
3chain C and (resseq 5:449 )CC
4chain D and (resseq 5:449 )DD

NCS oper:
IDCodeMatrixVector
1given(-0.987306, -0.004251, -0.158776), (0.001283, -0.999823, 0.018785), (-0.158828, 0.018343, 0.987136)92.390297, 213.705994, 5.40513
2given(0.894149, 0.422611, 0.147981), (0.422186, -0.9058, 0.035842), (0.149189, 0.030428, -0.98834)-43.5923, 184.498001, 31.882601
3given(-0.908735, -0.417249, 0.01021), (-0.417216, 0.907446, -0.049714), (0.011478, -0.049436, -0.998711)129.595001, 29.581301, 46.846901

-
Components

#1: Protein
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase


Mass: 51225.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS1519, BA_1636, GBAA1636, GBAA_1636 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q6I0U5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCLONING ERROR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 20% PEG 3350,100mM Na Formate,100mM Li Sulfate, 100mM Bis-Tris, pH 7, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 108118 / Num. obs: 106929 / % possible obs: 98.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.097 / Χ2: 1.016 / Net I/σ(I): 9.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.2 / Num. unique all: 10035 / Χ2: 0.984 / % possible all: 93.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→34.85 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.25 / σ(F): 1.44 / σ(I): 2.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 5314 4.99 %
Rwork0.156 --
obs0.158 106428 98.92 %
all-107612 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.827 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 330.23 Å2 / Biso mean: 36.71 Å2 / Biso min: 6.43 Å2
Baniso -1Baniso -2Baniso -3
1-8.808 Å2-0 Å2-4.238 Å2
2---9.932 Å2-0 Å2
3---1.124 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14124 0 48 1038 15210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114663
X-RAY DIFFRACTIONf_angle_d1.22519832
X-RAY DIFFRACTIONf_chiral_restr0.0922122
X-RAY DIFFRACTIONf_plane_restr0.0062581
X-RAY DIFFRACTIONf_dihedral_angle_d14.415540
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3419X-RAY DIFFRACTIONPOSITIONAL0.411
12B3419X-RAY DIFFRACTIONPOSITIONAL0.411
13C3394X-RAY DIFFRACTIONPOSITIONAL0.321
14D3430X-RAY DIFFRACTIONPOSITIONAL0.432
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.1230.2965050.244951610021951693.3
2.123-2.2080.2625080.20810007105151000798
2.208-2.3090.2315180.18810217107351021799.9
2.309-2.430.2425060.18102241073010224100
2.43-2.5830.2155510.17101861073710186100
2.583-2.7820.225380.168101711070910171100
2.782-3.0620.2015560.16710199107551019999.9
3.062-3.5040.2015390.15310227107661022799.8
3.504-4.4140.1435590.11710142107011014299.1
4.414-34.8550.1575340.13510225107591022599.2
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)
10.0930.72480.28355.71482.47531.26960.0908-0.204-0.0483-0.40190.0258-0.5654-0.2541-0.0288-0.16950.2294-0.043-0.05870.21560.01970.541760.9128144.185520.0895
20.7428-0.38350.04011.5651-0.1810.342-0.01390.12660.1803-0.1089-0.0377-0.14010.00020.00810.04360.08670.0007-0.01370.1080.05640.16338.5714129.500610.9163
30.5118-0.32620.13121.4313-0.26280.13350.06720.10650.0907-0.3173-0.07110.12770.0261-0.0337-0.00630.21420.0164-0.03610.19690.050.219632.7345124.25174.3721
40.8873-0.75770.01551.27250.17410.27450.18910.22280.5014-0.57-0.1712-0.8284-0.02890.1615-0.00420.38870.03440.22990.29630.20010.548755.9554134.6225-5.865
50.3915-0.6667-0.00951.36290.26060.25780.0248-0.0328-0.084-0.1843-0.01550.5084-0.0594-0.03820.00690.1404-0.0250.01220.1879-0.02530.321228.73970.88518.5846
60.1473-0.22350.06391.0491-0.00520.3026-0.01590.0336-0.095-0.1576-0.0709-0.18920.09320.08240.08560.09460.03060.05540.1315-0.0090.221454.383270.424413.8504
70.4923-0.32960.1031.4014-0.24190.20410.01810.08360.0499-0.2668-0.0766-0.2815-0.02410.07210.04520.12990.00740.06080.15230.02640.180555.826892.10498.3028
80.1998-0.10610.10761.50990.00150.18260.04810.1238-0.1216-0.6332-0.08620.2737-0.057-0.01910.02070.4130.0342-0.06890.2425-0.0680.21937.629579.2132-6.9048
90.01850.0398-0.05310.3672-0.14850.1833-0.1058-0.0754-0.01720.0740.0615-0.35380.00710.09690.06510.18370.0405-0.00280.31010.07170.478975.072379.979125.1952
100.3735-0.18930.00010.7338-0.11970.3013-0.02640.009-0.18150.14490.0026-0.06520.0778-0.00210.01890.11910.03710.01450.12650.01560.225651.077870.322930.1223
110.4744-0.23180.07271.5163-0.03750.2367-0.1111-0.0364-0.03790.33630.07190.0549-0.0481-0.0130.02310.14820.03170.03080.11960.00930.113640.242289.811834.2669
120.2477-0.32860.06751.2514-0.08110.3785-0.2031-0.15090.02080.64190.1358-0.5134-0.07010.09260.03420.44070.0903-0.17320.22450.00430.255961.579985.437850.3893
130.37880.6757-0.11081.54170.17960.45290.04650.30550.26110.14940.08220.42740.0503-0.1506-0.11010.17330.0286-0.00160.28340.11730.431715.9808132.013620.2361
140.6752-0.0879-0.01150.8774-0.50380.2928-0.0312-0.00370.31110.32710.0436-0.2072-0.22750.02150.00210.25440.0332-0.0630.1412-0.00130.371736.779144.094228.4446
150.4689-0.1502-0.00771.6552-0.33510.1056-0.1568-0.07990.12930.46080.0948-0.253-0.09510.03080.06130.27560.0381-0.09940.1262-0.01630.199545.7844119.834237.1856
160.7406-0.3395-0.34471.5681-0.14840.5316-0.1352-0.07120.2310.56350.1603-0.025-0.12090.0135-0.03090.35210.0666-0.03380.1738-0.00960.20933.7729131.953439.4025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -1:30)A-1 - 30
2X-RAY DIFFRACTION2(chain A and resid 31:188)A31 - 188
3X-RAY DIFFRACTION3(chain A and resid 189:346)A189 - 346
4X-RAY DIFFRACTION4(chain A and resid 347:449)A347 - 449
5X-RAY DIFFRACTION5(chain B and resid 1:30)B1 - 30
6X-RAY DIFFRACTION6(chain B and resid 31:104)B31 - 104
7X-RAY DIFFRACTION7(chain B and resid 105:347)B105 - 347
8X-RAY DIFFRACTION8(chain B and resid 348:449)B348 - 449
9X-RAY DIFFRACTION9(chain C and resid -1:30)C-1 - 30
10X-RAY DIFFRACTION10(chain C and resid 31:104)C31 - 104
11X-RAY DIFFRACTION11(chain C and resid 105:341)C105 - 341
12X-RAY DIFFRACTION12(chain C and resid 342:449)C342 - 449
13X-RAY DIFFRACTION13(chain D and resid 4:31)D4 - 31
14X-RAY DIFFRACTION14(chain D and resid 32:104)D32 - 104
15X-RAY DIFFRACTION15(chain D and resid 105:270)D105 - 270
16X-RAY DIFFRACTION16(chain D and resid 271:449)D271 - 449

+
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