[English] 日本語
Yorodumi
- PDB-4n8l: E249D mutant, RipA structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n8l
TitleE249D mutant, RipA structure
ComponentsPutative 4-hydroxybutyrate coenzyme A transferase
KeywordsTRANSFERASE / Coenzyme A transferase
Function / homology
Function and homology information


acetate CoA-transferase activity / acetate metabolic process
Similarity search - Function
Acetyl-CoA hydrolase/transferase, N-terminal / Acetyl-CoA hydrolase/transferase C-terminal domain / Acetyl-CoA hydrolase/transferase, C-terminal domain superfamily / Acetyl-CoA hydrolase/transferase / Acetyl-CoA hydrolase/transferase N-terminal domain / Acetyl-CoA hydrolase/transferase C-terminal domain / NagB/RpiA transferase-like
Similarity search - Domain/homology
4-hydroxybutyrate coenzyme A transferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.817 Å
AuthorsTorres, R. / Goulding, C.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural snapshots along the reaction pathway of Yersinia pestis RipA, a putative butyryl-CoA transferase.
Authors: Torres, R. / Lan, B. / Latif, Y. / Chim, N. / Goulding, C.W.
History
DepositionOct 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative 4-hydroxybutyrate coenzyme A transferase
B: Putative 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)104,5412
Polymers104,5412
Non-polymers00
Water55831
1
A: Putative 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2701
Polymers52,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative 4-hydroxybutyrate coenzyme A transferase


Theoretical massNumber of molelcules
Total (without water)52,2701
Polymers52,2701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)197.241, 197.241, 59.223
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Putative 4-hydroxybutyrate coenzyme A transferase / Putative Coenzyme A transferase / Similar to 4-hydroxybutyrate CoA transferase


Mass: 52270.324 Da / Num. of mol.: 2 / Mutation: E249D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: aCH1, y2385, YPO1926, YP_1668 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZC36
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis Tris, 27% PEG monomethyl ether 2000, and 1mM propionyl-CoA, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 11.3 % / Number: 362778 / Rmerge(I) obs: 0.147 / Χ2: 1.09 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 32116 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.595099.710.0751.02310.7
6.037.5910010.1031.07911.2
5.276.0310010.1190.95911.3
4.795.2710010.1281.0811.4
4.444.7910010.1361.0711.3
4.184.4410010.1451.0811.4
3.974.1810010.151.06611.4
3.83.9710010.1631.09511.4
3.653.810010.181.03711.4
3.533.6510010.2051.04811.4
3.423.5310010.2221.0911.3
3.323.4210010.261.11711.3
3.233.3210010.2961.07411.3
3.153.2310010.3371.11311.3
3.083.1510010.3821.10911.3
3.023.0810010.4431.07911.3
2.963.0210010.511.12611.3
2.92.9610010.5831.1811.2
2.852.910010.6751.15611.3
2.82.8510010.8021.14811.2
ReflectionResolution: 2.8→50 Å / Num. obs: 32103 / % possible obs: 99.87 % / Redundancy: 11.3 % / Biso Wilson estimate: 66.59 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 18.02
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.851100
2.85-2.91100
2.9-2.961100
2.96-3.021100
3.02-3.081100
3.08-3.151100
3.15-3.231100
3.23-3.321100
3.32-3.421100
3.42-3.531100
3.53-3.651100
3.65-3.81100
3.8-3.971100
3.97-4.181100
4.18-4.441100
4.44-4.791100
4.79-5.271100
5.27-6.031100
6.03-7.591100
7.59-50199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QLK

3qlk


Resolution: 2.817→42.704 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8458 / SU ML: 0.3 / Cross valid method: Free R / σ(F): 0 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1949 6.19 %Random
Rwork0.182 ---
obs0.1843 31507 98.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 281.04 Å2 / Biso mean: 87.0692 Å2 / Biso min: 33.87 Å2
Refinement stepCycle: LAST / Resolution: 2.817→42.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 0 31 6693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046786
X-RAY DIFFRACTIONf_angle_d0.9759206
X-RAY DIFFRACTIONf_chiral_restr0.0381056
X-RAY DIFFRACTIONf_plane_restr0.0041210
X-RAY DIFFRACTIONf_dihedral_angle_d13.3332528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.817-2.88740.27671310.26581901203290
2.8874-2.96550.29911370.24492020215794
2.9655-3.05270.26341340.23582023215795
3.0527-3.15120.27271350.22692083221897
3.1512-3.26380.26061350.22272078221398
3.2638-3.39440.29111380.21092110224899
3.3944-3.54880.21411460.19922140228699
3.5488-3.73580.23761390.187921482287100
3.7358-3.96970.21911450.181921492294100
3.9697-4.2760.22561420.164721512293100
4.276-4.70580.18251410.151121362277100
4.7058-5.38560.21311410.156821862327100
5.3856-6.78090.18211390.181721832322100
6.7809-42.70880.19561460.167222502396100
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)
11.88750.73931.31922.01881.20052.2088-0.0669-0.44250.37010.3164-0.0735-0.0047-0.0594-0.08450.11360.4296-0.0891-0.01410.6304-0.16430.404949.5032-54.724529.28
22.5295-0.6823-0.51531.1555-0.49421.30660.02580.13920.4501-0.251-0.01380.0828-0.0632-0.0709-0.02280.3859-0.09760.0040.4688-0.04530.367353.3677-57.08014.6492
32.4037-0.2558-0.63441.9079-0.42211.1964-0.0346-0.13150.1820.0207-0.0623-0.6843-0.03310.42120.08370.4084-0.1074-0.00680.65540.03520.740775.1128-63.67937.6748
42.27890.27420.07731.8839-0.01520.696-0.07770.2658-0.307-0.1150.0044-0.34270.17920.15650.05720.46840.05320.20270.6072-0.02480.737782.0506-93.70913.5881
50.4998-0.6535-0.01551.66860.98491.1604-0.2841-0.1427-0.34810.56570.1921-1.0160.09790.4341-0.06140.78910.1672-0.08970.75070.11550.828577.933-94.741830.2351
61.5981-0.5009-0.5412.4022-0.38861.4852-0.1373-0.1356-0.24260.44760.0656-0.24370.0838-0.08040.01010.4848-0.01060.08640.55920.14640.591265.7626-97.248823.0364
71.34860.24960.40670.89790.76040.9077-0.29-0.37470.40680.74920.2207-0.98980.02590.1416-0.05590.80570.06-0.46210.8479-0.07421.001972.544-75.191731.526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 189 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 190 through 307 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 308 through 440 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 189 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 190 through 216 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 307 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 308 through 440 )B0

+
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