[English] 日本語
Yorodumi
- PDB-4c3y: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c3y
TitleCrystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Components3-KETOSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / ROSSMANN FOLD
Function / homology
Function and homology information


3-oxosteroid 1-dehydrogenase activity / steroid metabolic process / nucleotide binding
Similarity search - Function
Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ANDROSTA-1,4-DIENE-3,17-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / 3-ketosteroid dehydrogenase
Similarity search - Component
Biological speciesRHODOCOCCUS ERYTHROPOLIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsRohman, A. / van Oosterwijk, N. / Thunnissen, A.M.W.H. / Dijkstra, B.W.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure and Site-Directed Mutagenesis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1 Explain its Catalytic Mechanism
Authors: Rohman, A. / Van Oosterwijk, N. / Thunnissen, A.M.W.H. / Dijkstra, B.W.
#1: Journal: Acta Crystallogr., Sect.F / Year: 2012
Title: Purification, Crystallization and Preliminary X-Ray Crystallographic Analysis of 3-Ketosteroid Delta1-Dehydrogenase from Rhodococcus Erythropolis Sq1
Authors: Rohman, A. / Van Oosterwijk, N. / Dijkstra, B.W.
History
DepositionAug 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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.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_label_seq_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 / _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: 3-KETOSTEROID DEHYDROGENASE
B: 3-KETOSTEROID DEHYDROGENASE
C: 3-KETOSTEROID DEHYDROGENASE
D: 3-KETOSTEROID DEHYDROGENASE
E: 3-KETOSTEROID DEHYDROGENASE
F: 3-KETOSTEROID DEHYDROGENASE
G: 3-KETOSTEROID DEHYDROGENASE
H: 3-KETOSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,91434
Polymers442,0978
Non-polymers9,81726
Water25,4731414
1
A: 3-KETOSTEROID DEHYDROGENASE
B: 3-KETOSTEROID DEHYDROGENASE
C: 3-KETOSTEROID DEHYDROGENASE
D: 3-KETOSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,95717
Polymers221,0484
Non-polymers4,90813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16650 Å2
ΔGint-58.1 kcal/mol
Surface area64230 Å2
MethodPISA
2
E: 3-KETOSTEROID DEHYDROGENASE
F: 3-KETOSTEROID DEHYDROGENASE
G: 3-KETOSTEROID DEHYDROGENASE
H: 3-KETOSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,95717
Polymers221,0484
Non-polymers4,90813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16370 Å2
ΔGint-58 kcal/mol
Surface area64360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.747, 132.142, 363.597
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
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 3 - 510 / Label seq-ID: 23 - 530

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
3-KETOSTEROID DEHYDROGENASE / 3-KETOSTEROID DELTA1-DEHYDROGENASE


Mass: 55262.109 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOCOCCUS ERYTHROPOLIS (bacteria) / Strain: SQ1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RA02, 3-oxosteroid 1-dehydrogenase

-
Non-polymers , 5 types, 1440 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-ANB / ANDROSTA-1,4-DIENE-3,17-DIONE


Mass: 284.393 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H24O2 / Comment: hormone*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1414 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsTETRAETHYLENE GLYCOL (PG4): THE MOLECULES ARE FROM CRYSTALLIZATION BUFFER FLAVIN-ADENINE ...TETRAETHYLENE GLYCOL (PG4): THE MOLECULES ARE FROM CRYSTALLIZATION BUFFER FLAVIN-ADENINE DINUCLEOTIDE (FAD): THE MOLECULES ARE NATIVELY BOUND TO THE PROTEIN ANDROSTA-1,4-DIENE-3,17-DIONE (ANB): THE MOLECULES ARE FROM CO-CRYSTALLIZATION SODIUM ION (NA): THE IONS ARE MOST LIKELY FROM PROTEIN STORAGE BUFFER
Sequence detailsAN N-TERMINUS HIS6-TAG AND LINKER, MGSSHHHHHHSSGLVPRGSH, WAS ADDED TO THE PROTEIN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57 %
Description: THE STRUCTURE WAS DETERMINED BY RIGID BODY REFINEMENT USING THE NATIVE STRUCTURE WITH THE PROGRAM REFMAC5
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% (V/V) PEG (POLYETHYLENE GLYCOL) 400, 0.1 M HEPES (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) BUFFER PH 7.5, 2.0 M AMMONIUM SULFATE. SITTING DROP. TEMPERATURE 293 K. THE PROTEIN ...Details: 2% (V/V) PEG (POLYETHYLENE GLYCOL) 400, 0.1 M HEPES (4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID) BUFFER PH 7.5, 2.0 M AMMONIUM SULFATE. SITTING DROP. TEMPERATURE 293 K. THE PROTEIN SOLUTION SAMPLE WAS INCUBATED WITH 1,4-ANDROSTADIENE-3,17-DIONE POWDER ON ICE FOR 3 H PRIOR TO THE CRYSTALLIZATION EXPERIMENT.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.3→49.42 Å / Num. obs: 229728 / % possible obs: 99.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.3→49.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.186 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24882 11485 5 %RANDOM
Rwork0.21045 ---
obs0.21236 217960 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.418 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29620 0 674 1414 31708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0230900
X-RAY DIFFRACTIONr_bond_other_d0.0070.0229124
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.99342070
X-RAY DIFFRACTIONr_angle_other_deg2.7433.00866192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66754040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84524.261324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.761154492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.83715224
X-RAY DIFFRACTIONr_chiral_restr0.0720.24608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02135980
X-RAY DIFFRACTIONr_gen_planes_other0.0070.026740
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A307890.05
12B307890.05
21A310480.05
22C310480.05
31A309850.05
32D309850.05
41A311470.04
42E311470.04
51A309070.05
52F309070.05
61A308670.05
62G308670.05
71A309740.05
72H309740.05
81B308420.05
82C308420.05
91B308940.05
92D308940.05
101B307290.05
102E307290.05
111B309360.05
112F309360.05
121B306710.06
122G306710.06
131B307750.05
132H307750.05
141C308650.05
142D308650.05
151C309940.05
152E309940.05
161C309250.05
162F309250.05
171C309340.05
172G309340.05
181C308510.05
182H308510.05
191D311200.05
192E311200.05
201D310840.04
202F310840.04
211D307870.06
212G307870.06
221D310150.05
222H310150.05
231E309070.05
232F309070.05
241E309330.04
242G309330.04
251E310050.05
252H310050.05
261F307960.05
262G307960.05
271F309760.05
272H309760.05
281G307060.06
282H307060.06
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 761 -
Rwork0.357 14707 -
obs--95.87 %

+
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