[English] 日本語
Yorodumi
- PDB-3i4f: Structure of putative 3-oxoacyl-reductase from bacillus thuringiensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i4f
TitleStructure of putative 3-oxoacyl-reductase from bacillus thuringiensis
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / structural genomics / 3-oxoacyl-reductase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus thuringiensis serovar kurstaki (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 Å
AuthorsRamagopal, U.A. / Kim, J. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of putative 3-oxoacyl-reductase from bacillus thuringiensis
Authors: Ramagopal, U.A. / Kim, J. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase


Theoretical massNumber of molelcules
Total (without water)118,3954
Polymers118,3954
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-53 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.418, 86.592, 78.413
Angle α, β, γ (deg.)90.000, 97.050, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] reductase


Mass: 29598.635 Da / Num. of mol.: 4 / Fragment: sequence database residues 37-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar kurstaki (bacteria)
Strain: T03a001 / Gene: bthur0006_42590 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3ERL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Acetate pH 4.5, 30% PEG400, 0.2M Calcium Acetate monohydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 36162 / Num. obs: 36162 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.087 / Χ2: 1.189 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.494.20.44935320.91197.5
2.49-2.594.30.41335690.953199.1
2.59-2.74.40.33236030.9271100
2.7-2.854.40.23936351.0221100
2.85-3.024.40.16436271.0851100
3.02-3.264.40.12836081.2181100
3.26-3.584.30.08736211.2571100
3.58-4.14.20.06836601.4661100
4.1-5.174.10.05636201.38199.9
5.17-503.90.05636871.743198.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.39→27.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.247 / WRfactor Rwork: 0.191 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.807 / SU B: 20.008 / SU ML: 0.209 / SU R Cruickshank DPI: 0.633 / SU Rfree: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.633 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1841 5.1 %RANDOM
Rwork0.192 ---
obs0.195 36140 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.98 Å2 / Biso mean: 38.086 Å2 / Biso min: 19.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å2-1.54 Å2
2---0.42 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.39→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7467 0 0 60 7527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227603
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.9510271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.7724.59329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.367151346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4241536
X-RAY DIFFRACTIONr_chiral_restr0.080.21191
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025600
X-RAY DIFFRACTIONr_mcbond_it0.4691.54765
X-RAY DIFFRACTIONr_mcangle_it0.91127659
X-RAY DIFFRACTIONr_scbond_it1.38932838
X-RAY DIFFRACTIONr_scangle_it2.4224.52610
LS refinement shellResolution: 2.39→2.456 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 116 -
Rwork0.258 2368 -
all-2484 -
obs--93.56 %
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)
12.5209-0.01510.51851.32990.0492.0477-0.04160.456-0.0904-0.01980.0891-0.140.13290.1028-0.04750.0184-0.01820.00340.1503-0.0040.031624.548-3.10618.742
21.46830.21580.19691.29150.16052.15930.0799-0.2277-0.08630.0618-0.0316-0.0110.131-0.0552-0.04830.0221-0.01530.01060.09520.0130.03910.142-2.16757.209
31.64770.01670.22911.6151-0.21371.9522-0.00910.24860.2091-0.00110.03290.0925-0.1005-0.0757-0.02380.0061-0.0021-0.00250.10420.05460.0552-6.0073.44724.42
41.25530.04970.37271.4687-0.04671.81180.0512-0.11960.18350.01640.018-0.0309-0.03680.1381-0.06910.0038-0.00990.01090.0864-0.01090.044630.6684.24751.176
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 286
2X-RAY DIFFRACTION2B37 - 286
3X-RAY DIFFRACTION3C37 - 286
4X-RAY DIFFRACTION4D37 - 286

+
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