[English] 日本語
Yorodumi
- PDB-4l7k: Crystal Structure of Ketosteroid Isomerase D38E from Pseudomonas ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l7k
TitleCrystal Structure of Ketosteroid Isomerase D38E from Pseudomonas Testosteroni (tKSI)
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Use of anion-aromatic interactions to position the general base in the ketosteroid isomerase active site.
Authors: Schwans, J.P. / Sunden, F. / Lassila, J.K. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionJun 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
E: Steroid Delta-isomerase
F: Steroid Delta-isomerase
G: Steroid Delta-isomerase
H: Steroid Delta-isomerase
I: Steroid Delta-isomerase
J: Steroid Delta-isomerase
K: Steroid Delta-isomerase
O: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,47368
Polymers161,11412
Non-polymers5,36056
Water16,232901
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,00114
Polymers26,8522
Non-polymers1,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-129 kcal/mol
Surface area11760 Å2
MethodPISA
2
C: Steroid Delta-isomerase
J: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,71311
Polymers26,8522
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-93 kcal/mol
Surface area11880 Å2
MethodPISA
3
D: Steroid Delta-isomerase
I: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,71311
Polymers26,8522
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-90 kcal/mol
Surface area11970 Å2
MethodPISA
4
E: Steroid Delta-isomerase
G: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,61710
Polymers26,8522
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-93 kcal/mol
Surface area12210 Å2
MethodPISA
5
F: Steroid Delta-isomerase
K: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,90513
Polymers26,8522
Non-polymers1,05311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-113 kcal/mol
Surface area11840 Å2
MethodPISA
6
H: Steroid Delta-isomerase
O: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5259
Polymers26,8522
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-90 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.128, 111.128, 499.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein
Steroid Delta-isomerase / / Delta(5)-3-ketosteroid isomerase


Mass: 13426.128 Da / Num. of mol.: 12 / Mutation: D38E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATC 11996 / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 5mg/ml protein, 1.6 M ammonium sulfate, 40mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9795
SYNCHROTRONSSRL BL9-120.9795
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMar 24, 2010Si double crystal
ADSC QUANTUM 315r2CCDMay 10, 2010Si single crystal
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si double crystalSINGLE WAVELENGTHx-ray1
2Si single crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→29.937 Å / Num. all: 107620 / Num. obs: 107620 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Rsym value: 0.137 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.2110.70.7281.1164349153600.72899.7
2.21-2.3514.10.6821206735146130.682100
2.35-2.5121.80.6351.1299763137780.635100
2.51-2.7121.70.4371.7279474128980.437100
2.71-2.9721.60.2652.8256602118810.265100
2.97-3.3221.40.1445232135108250.144100
3.32-3.8421.10.0848.220334396500.084100
3.84-4.720.70.05510.617036182440.055100
4.7-6.6420.10.0511.813118865250.05100
6.64-29.93719.10.032147354638460.03298.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å29.26 Å
Translation2.4 Å29.26 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.26 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.354 / WRfactor Rwork: 0.3029 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.5953 / SU B: 22.244 / SU ML: 0.262 / SU R Cruickshank DPI: 0.3269 / SU Rfree: 0.2688 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.354 5363 5 %RANDOM
Rwork0.3029 ---
obs0.3055 107450 99.96 %-
all-107450 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 199.32 Å2 / Biso mean: 33.8882 Å2 / Biso min: 12.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.71 Å20 Å2
2--1.41 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11276 0 285 901 12462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212177
X-RAY DIFFRACTIONr_bond_other_d0.0040.027915
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.96416591
X-RAY DIFFRACTIONr_angle_other_deg2.064319218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23751560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13523.617564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.615151869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6371596
X-RAY DIFFRACTIONr_chiral_restr0.0640.21833
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113849
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022575
X-RAY DIFFRACTIONr_mcbond_it0.3261.57662
X-RAY DIFFRACTIONr_mcbond_other0.0821.53104
X-RAY DIFFRACTIONr_mcangle_it0.598212295
X-RAY DIFFRACTIONr_scbond_it0.92134515
X-RAY DIFFRACTIONr_scangle_it1.524.54296
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 368 -
Rwork0.349 7324 -
all-7692 -
obs--99.57 %
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)
10.62730.07350.05471.32410.11362.2097-0.02170.08770.0728-0.1808-0.0654-0.016-0.41020.19980.08710.2914-0.0109-0.09440.05720.01540.089437.559467.0592120.9012
20.77660.28380.43211.40740.34792.91730.02640.05670.00370.0757-0.10610.02090.09830.09110.07960.22830.0121-0.05430.0232-0.00210.177935.369252.168139.246
30.73110.06120.18620.94270.0152.0407-0.11530.0908-0.11060.09990.1575-0.0097-0.0570.2467-0.04220.10970.1176-0.03370.308-0.04450.081248.040559.7909193.849
41.26-0.83290.69020.6982-0.56971.43670.1294-0.09010.10290.0967-0.0327-0.1150.0602-0.2032-0.09670.4623-0.1091-0.09160.1364-0.00460.2329-23.3599126.1975159.6756
50.9923-0.90970.83561.3296-0.35021.86080.1734-0.12940.14130.1618-0.0564-0.18240.355-0.1665-0.1170.5053-0.2283-0.01420.1152-0.0140.071732.770994.0326159.479
61.0915-0.22120.69711.35870.04873.658-0.04170.12080.1623-0.1906-0.0853-0.0663-0.21360.39720.1270.193-0.0436-0.02190.05810.04120.183493.286135.009120.9282
71.6759-0.5037-0.14361.7314-1.21911.90620.0132-0.19460.13-0.27160.0059-0.1859-0.38610.3786-0.01910.5248-0.20250.01630.1734-0.06450.146647.397375.4181163.8535
80.4642-0.8619-0.38212.22540.34562.1598-0.1591-0.0826-0.04130.07730.03020.06810.011-0.74660.12890.14690.08450.00660.6311-0.13540.21277.928328.8424168.9979
91.5155-0.7433-0.1661.6306-0.80791.4631-0.1167-0.10920.0508-0.1769-0.0436-0.2038-0.35180.30250.16030.4156-0.103-0.08290.1477-0.01430.292-8.6178107.7608163.9634
101.1575-0.03070.32421.30270.84142.412-0.03210.0276-0.01710.22390.01630.25280.12460.00520.01580.16830.12420.02050.13830.01510.117634.130965.217212.3616
110.73580.00960.41711.2744-0.00682.7598-0.0006-0.04020.04520.0706-0.1064-0.01050.30230.0770.10710.1746-0.03390.00830.0499-0.00720.183191.21520.0145139.1643
120.2451-0.21660.26391.99980.29182.29480.05320.3577-0.08110.07390.01840.04730.03830.2449-0.07160.03990.1461-0.04320.6737-0.16770.057368.974450.7131173.7028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3C1 - 125
4X-RAY DIFFRACTION4D1 - 125
5X-RAY DIFFRACTION5E1 - 125
6X-RAY DIFFRACTION6F1 - 125
7X-RAY DIFFRACTION7G1 - 125
8X-RAY DIFFRACTION8H1 - 125
9X-RAY DIFFRACTION9I1 - 125
10X-RAY DIFFRACTION10J1 - 125
11X-RAY DIFFRACTION11K1 - 125
12X-RAY DIFFRACTION12O1 - 125

+
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