[English] 日本語
Yorodumi
- PDB-6s4g: Crystal structure of the omega transaminase from Chromobacterium ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6s4g
TitleCrystal structure of the omega transaminase from Chromobacterium violaceum in complex with PMP
ComponentsProbable aminotransferase
KeywordsTRANSFERASE / Transaminase / PMP / PLP-dependent enzyme / Complex
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase activity / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Putative 8-amino-7-oxononanoate synthase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.67 Å
AuthorsRuggieri, F. / Campillo Brocal, J.C. / Humble, M.S. / Walse, B. / Logan, D.T. / Berglund, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Union634200 Sweden
CitationJournal: Sci Rep / Year: 2019
Title: Insight into the dimer dissociation process of the Chromobacterium violaceum (S)-selective amine transaminase.
Authors: Ruggieri, F. / Campillo-Brocal, J.C. / Chen, S. / Humble, M.S. / Walse, B. / Logan, D.T. / Berglund, P.
History
DepositionJun 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 / refine / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable aminotransferase
B: Probable aminotransferase
C: Probable aminotransferase
D: Probable aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,94815
Polymers208,4334
Non-polymers1,51511
Water8,629479
1
A: Probable aminotransferase
B: Probable aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9437
Polymers104,2162
Non-polymers7275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12650 Å2
ΔGint-63 kcal/mol
Surface area27720 Å2
MethodPISA
2
C: Probable aminotransferase
D: Probable aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0058
Polymers104,2162
Non-polymers7896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12940 Å2
ΔGint-56 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.909, 61.973, 118.810
Angle α, β, γ (deg.)75.070, 81.310, 75.300
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA6 - 45812 - 464
21THRTHRLEULEUBB6 - 45812 - 464
12THRTHRGLYGLYAA6 - 45712 - 463
22THRTHRGLYGLYCC6 - 45712 - 463
13THRTHRGLYGLYAA6 - 45712 - 463
23THRTHRGLYGLYDD6 - 45712 - 463
14THRTHRGLYGLYBB6 - 45712 - 463
24THRTHRGLYGLYCC6 - 45712 - 463
15THRTHRGLYGLYBB6 - 45712 - 463
25THRTHRGLYGLYDD6 - 45712 - 463
16ARGARGGLYGLYCC5 - 45711 - 463
26ARGARGGLYGLYDD5 - 45711 - 463

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Probable aminotransferase / (S)-selective amine transaminase / omega-transaminase


Mass: 52108.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (bacteria)
Gene: CV_2025 / Plasmid: pET8a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7NWG4, adenosylmethionine-8-amino-7-oxononanoate 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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Drops of 200 nl protein at 7.5 mg/ml mixed with 200 nl of 100 mM HEPES pH 7.5, 350 mM NaCl, 22.5 % w/v PEG 4000, 0.1 mM PLP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.67→48.04 Å / Num. obs: 172591 / % possible obs: 91.9 % / Redundancy: 2.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.061 / Rrim(I) all: 0.111 / Net I/σ(I): 5.3 / Num. measured all: 413858 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.67-1.72.30.6461836180790.6540.480.811.487
9.14-48.042.80.06727719840.9950.0380.07710.986.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_TRA
Highest resolutionLowest resolution
Rotation8.11 Å48.04 Å
Translation8.11 Å48.04 Å

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A6T

4a6t


Resolution: 1.67→48.09 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1997 / WRfactor Rwork: 0.1729 / FOM work R set: 0.8533 / SU B: 4.677 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1058 / SU Rfree: 0.0971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 8608 5 %RANDOM
Rwork0.1606 ---
obs0.1618 163935 91.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.83 Å2 / Biso mean: 25.689 Å2 / Biso min: 11.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20.01 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.67→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14255 0 98 479 14832
Biso mean--29.36 25.39 -
Num. residues----1815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314740
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713483
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.64119946
X-RAY DIFFRACTIONr_angle_other_deg1.5381.57731106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06851815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88921.122820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.143152359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.88115118
X-RAY DIFFRACTIONr_chiral_restr0.0930.21802
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216761
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023422
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A149880.07
12B149880.07
21A149770.07
22C149770.07
31A150350.07
32D150350.07
41B148870.08
42C148870.08
51B150030.07
52D150030.07
61C149920.08
62D149920.08
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 619 -
Rwork0.264 11922 -
all-12541 -
obs--90.63 %
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)
11.24950.5697-0.34990.9920.13761.15180.0509-0.10070.20460.02310.0140.0706-0.1330.0425-0.0650.0427-0.0030.0270.1192-0.03480.0507-26.38816.42852.433
21.06780.23140.00650.52810.40581.29740.0243-0.07340.01590.03030.0149-0.05110.03960.1801-0.03910.011-0.00690.0120.1112-0.00390.0336-11.3066.06826.037
30.60040.1308-0.08161.10990.45320.7001-0.001-0.00840.02670.03890.0030.02340.009-0.0487-0.00190.0041-0.00060.00330.0345-0.00290.0044-27.11834.583-5.424
40.84680.14620.22490.85160.41580.86150.03290.1077-0.1271-0.14530.0802-0.19930.03450.1338-0.1130.05630.00370.04050.0847-0.04020.0714-12.21820.163-29.652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 501
2X-RAY DIFFRACTION2B6 - 501
3X-RAY DIFFRACTION3C5 - 501
4X-RAY DIFFRACTION4D5 - 501

+
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://pdbjlvh1.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