[English] 日本語
Yorodumi
- PDB-3bb9: Crystal structure of a putative ketosteroid isomerase (sfri_1973)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bb9
TitleCrystal structure of a putative ketosteroid isomerase (sfri_1973) from shewanella frigidimarina ncimb 400 at 1.80 A resolution
ComponentsPutative orphan protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Putative orphan protein
Function and homology information
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ketosteroid isomerase (YP_750657.1) from Shewanella frigidimarina NCIMB 400 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: 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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative orphan protein
B: Putative orphan protein
C: Putative orphan protein
D: Putative orphan protein
E: Putative orphan protein
F: Putative orphan protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,97016
Polymers98,3496
Non-polymers62110
Water11,007611
1
A: Putative orphan protein
B: Putative orphan protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0316
Polymers32,7832
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
MethodPISA
2
C: Putative orphan protein
D: Putative orphan protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0937
Polymers32,7832
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
MethodPISA
3
E: Putative orphan protein
F: Putative orphan protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8453
Polymers32,7832
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.558, 113.820, 137.132
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 28 - 147 / Label seq-ID: 29 - 148

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein
Putative orphan protein


Mass: 16391.559 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Strain: NCIMB 400 / Gene: YP_750657.1, Sfri_1973 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q082J6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.689 Å3/Da / Density % sol: 27.155 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: NANODROP, 0.2M K/Na Tartrate, 20.0% PEG 3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97971
ReflectionResolution: 1.8→29.361 Å / Num. obs: 61505 / % possible obs: 98.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.853.10.8330.91322142170.83392.3
1.85-1.93.20.6691.11384243100.66997.3
1.9-1.953.40.5081.11404441690.50896.3
1.95-2.013.40.38321410041440.38398.1
2.01-2.083.50.322.41392040070.3298.7
2.08-2.153.50.272.81375738990.2797.8
2.15-2.233.50.2263.31335037690.22698.6
2.23-2.323.50.1913.71294836560.19199.4
2.32-2.433.50.1724.41237034980.17298.8
2.43-2.553.50.1355.51197333800.13599
2.55-2.683.50.1156.41132532110.11599.3
2.68-2.853.50.0957.71073530650.09599.4
2.85-3.043.50.0828.61009328860.08299.5
3.04-3.293.50.06610.6941126890.06699.4
3.29-3.63.50.05212.7853124680.05299.5
3.6-4.023.30.04813.4742922350.04898.9
4.02-4.653.10.04514616919970.04598.1
4.65-5.693.50.04912.4600217350.04999.9
5.69-8.053.50.04913.5473613700.04999.8
8.05-29.3613.20.03815.925508000.03897.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.361 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.693 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ETHYLENE GLYCOL MOLECULES FROM THE CRYO CONDITIONS ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3117 5.1 %RANDOM
Rwork0.175 ---
obs0.178 61450 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.971 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5635 0 40 611 6286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215926
X-RAY DIFFRACTIONr_bond_other_d0.0010.023787
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9258033
X-RAY DIFFRACTIONr_angle_other_deg0.89639324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9255772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.52324.748238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.961151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.961519
X-RAY DIFFRACTIONr_chiral_restr0.0770.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021133
X-RAY DIFFRACTIONr_nbd_refined0.2090.31052
X-RAY DIFFRACTIONr_nbd_other0.1930.33901
X-RAY DIFFRACTIONr_nbtor_refined0.1730.52807
X-RAY DIFFRACTIONr_nbtor_other0.0930.53186
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5781
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1460.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.332
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.370
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.550
X-RAY DIFFRACTIONr_mcbond_it2.12333918
X-RAY DIFFRACTIONr_mcbond_other0.92531568
X-RAY DIFFRACTIONr_mcangle_it2.96356065
X-RAY DIFFRACTIONr_scbond_it5.26982350
X-RAY DIFFRACTIONr_scangle_it6.915111968
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A615MEDIUM POSITIONAL0.220.5
2B615MEDIUM POSITIONAL0.320.5
3C615MEDIUM POSITIONAL0.250.5
4D615MEDIUM POSITIONAL0.240.5
5E615MEDIUM POSITIONAL0.270.5
6F615MEDIUM POSITIONAL0.180.5
1A630LOOSE POSITIONAL0.415
2B630LOOSE POSITIONAL0.735
3C630LOOSE POSITIONAL0.435
4D630LOOSE POSITIONAL0.455
5E630LOOSE POSITIONAL0.555
6F630LOOSE POSITIONAL0.535
1A615MEDIUM THERMAL1.62
2B615MEDIUM THERMAL1.472
3C615MEDIUM THERMAL1.552
4D615MEDIUM THERMAL1.472
5E615MEDIUM THERMAL1.312
6F615MEDIUM THERMAL1.482
1A630LOOSE THERMAL3.2710
2B630LOOSE THERMAL3.1610
3C630LOOSE THERMAL3.0610
4D630LOOSE THERMAL2.9510
5E630LOOSE THERMAL2.7410
6F630LOOSE THERMAL3.3310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 239 -
Rwork0.274 3977 -
all-4216 -
obs--91.85 %
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)
11.54130.2113-0.62132.4407-1.24560.9339-0.07930.0126-0.1371-0.02170.2320.12130.0107-0.2586-0.1527-0.04970.0041-0.00290.00630.0252-0.02554.275188.653917.8935
20.1865-0.02980.03130.86770.16230.3608-0.0112-0.0216-0.00660.05150.026-0.0675-0.01780.0024-0.0148-0.0040.01770.0055-0.04310.0081-0.029520.7344103.176320.0082
31.75080.1308-1.13821.01480.22250.9886-0.04490.2244-0.0821-0.0513-0.0592-0.02860.0027-0.09170.1042-0.0631-0.00340.0011-0.0049-0.0042-0.04524.120172.996744.825
40.8123-0.25920.19722.0205-0.27180.74710.01570.030.01220.1952-0.03820.1915-0.07840.00770.0225-0.0415-0.01470.0303-0.0582-0.0203-0.0202-13.205178.91957.6223
50.3419-0.2891-0.17490.9720.12490.80940.0092-0.05840.09760.00690.0007-0.03190.01030.1736-0.0098-0.0411-0.00160.0034-0.0013-0.0018-0.031425.391462.725921.8049
60.66240.3476-0.18171.3067-0.63751.5897-0.0389-0.0104-0.0265-0.0607-0.04640.060.06070.02890.0853-0.04290.0250.0031-0.0617-0.0079-0.01899.854552.52139.6547
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 14724 - 148
2X-RAY DIFFRACTION2BB23 - 14724 - 148
3X-RAY DIFFRACTION3CC23 - 14724 - 148
4X-RAY DIFFRACTION4DD23 - 14724 - 148
5X-RAY DIFFRACTION5EE23 - 14724 - 148
6X-RAY DIFFRACTION6FF28 - 14729 - 148

+
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