[English] 日本語
Yorodumi
- PDB-5epa: Crystal structure of non-heme alpha ketoglutarate dependent carbo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5epa
TitleCrystal structure of non-heme alpha ketoglutarate dependent carbocyclase SnoK from nogalamycin biosynthesis
ComponentsSnoK
KeywordsLYASE / non-heme iron center / polyketide biosynthesis
Function / homology
Function and homology information


q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / SnoK
Similarity search - Component
Biological speciesStreptomyces nogalater (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSelvaraj, B. / Lindqvist, Y. / Siitonen, V. / Niiranen, L. / Metsa-Ketela, M. / Schneider, G.
Funding support Sweden, Finland, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Finnish Academy Finland
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.
Authors: Siitonen, V. / Selvaraj, B. / Niiranen, L. / Lindqvist, Y. / Schneider, G. / Metsa-Ketela, M.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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: SnoK
B: SnoK
C: SnoK
D: SnoK
E: SnoK
F: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,89921
Polymers187,6146
Non-polymers1,28515
Water17,997999
1
A: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4713
Polymers31,2691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4954
Polymers31,2691
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4713
Polymers31,2691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5205
Polymers31,2691
Non-polymers2514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4713
Polymers31,2691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: SnoK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4713
Polymers31,2691
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.009, 83.151, 271.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 5 - 262 / Label seq-ID: 17 - 274

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
SnoK / carbocyclase SnoK


Mass: 31269.061 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: snoK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RN60
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 999 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG MME 550, magnesium chloride, Tris/HCl, alpha ketoglutarate, ammonium ferric citrate
PH range: 8.0-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.24→47.7 Å / Num. obs: 96076 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.2
Reflection shellResolution: 2.24→2.32 Å / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.6 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EP9

5ep9


Resolution: 2.24→47.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.774 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.316 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22812 4146 5 %RANDOM
Rwork0.19332 ---
obs0.19504 78850 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.704 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--0.22 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.24→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12138 0 69 999 13206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912588
X-RAY DIFFRACTIONr_bond_other_d0.0080.0211695
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.95817119
X-RAY DIFFRACTIONr_angle_other_deg1.296326897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64651544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87922.812601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13151957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.15815124
X-RAY DIFFRACTIONr_chiral_restr0.0840.21877
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114238
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022878
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1521.3466173
X-RAY DIFFRACTIONr_mcbond_other1.1521.3466172
X-RAY DIFFRACTIONr_mcangle_it1.9472.0137706
X-RAY DIFFRACTIONr_mcangle_other1.9472.0137707
X-RAY DIFFRACTIONr_scbond_it1.8271.5496415
X-RAY DIFFRACTIONr_scbond_other1.8281.5496411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7692.2339406
X-RAY DIFFRACTIONr_long_range_B_refined6.54112.11914763
X-RAY DIFFRACTIONr_long_range_B_other6.46811.48814330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A157540.07
12B157540.07
21A157440.07
22C157440.07
31A157180.08
32D157180.08
41A156810.08
42E156810.08
51A153660.08
52F153660.08
61B157110.07
62C157110.07
71B156740.08
72D156740.08
81B157120.07
82E157120.07
91B155070.06
92F155070.06
101C158760.06
102D158760.06
111C157910.06
112E157910.06
121C154920.07
122F154920.07
131D157250.07
132E157250.07
141D154730.07
142F154730.07
151E155190.07
152F155190.07
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 271 -
Rwork0.296 5623 -
obs--96.56 %
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)
11.5261-0.0390.19261.1305-0.05361.5527-0.04960.08260.0206-0.0436-0.00280.0144-0.08150.01220.05250.0204-0.0119-0.0190.1199-0.04120.263337.8183.50213.573
23.12450.10240.50932.14480.52141.74430.01680.2603-0.025-0.13350.1083-0.1015-0.0740.1352-0.12520.0508-0.00140.0160.107-0.03070.2553.01440.10832.298
31.927-0.0568-0.19821.4057-0.12550.9563-0.0175-0.15550.02840.10590.0287-0.0288-0.00070.0395-0.01130.01090.0244-0.00860.1746-0.02490.27796.743-8.49154.986
41.7165-0.37090.25681.13270.03751.2272-0.0438-0.028-0.16710.0087-0.01980.08370.0528-0.04290.06350.00550.01230.00580.1319-0.01530.315217.18441.52740.808
51.52870.1268-0.12590.9478-0.04561.4856-0.016-0.02050.0588-0.0519-0.02040.0217-0.02650.05140.03650.00490.0084-0.01530.0769-0.02120.253447.003-1.549.604
64.12530.0783-0.07081.06860.19612.19850.0035-0.10010.0181-0.0550.03160.03440.1502-0.0941-0.03510.0852-0.0285-0.02710.2016-0.02410.34381.959-3.288.373
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 262
2X-RAY DIFFRACTION2B5 - 262
3X-RAY DIFFRACTION3C5 - 262
4X-RAY DIFFRACTION4D5 - 262
5X-RAY DIFFRACTION5E5 - 262
6X-RAY DIFFRACTION6F5 - 262

+
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