[English] 日本語
Yorodumi
- PDB-8fek: Crystal structure of PBP cyclase Ulm16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fek
TitleCrystal structure of PBP cyclase Ulm16
ComponentsPBP cyclase Ulm16
KeywordsHYDROLASE / Thioesterase / cyclase / heterochiral / Ulleungmycin
Function / homology: / Beta-lactamase-related / Beta-lactamase / Beta-lactamase/transpeptidase-like / Beta-lactamase
Function and homology information
Biological speciesStreptomyces sp. KCB13F003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.058 Å
AuthorsPatel, R. / Budimir, Z. / Parkinson, E. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138002 United States
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase.
Authors: Budimir, Z.L. / Patel, R.S. / Eggly, A. / Evans, C.N. / Rondon-Cordero, H.M. / Adams, J.J. / Das, C. / Parkinson, E.I.
History
DepositionDec 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PBP cyclase Ulm16


Theoretical massNumber of molelcules
Total (without water)44,7591
Polymers44,7591
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.822, 67.871, 56.779
Angle α, β, γ (deg.)90.00, 102.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PBP cyclase Ulm16 / Beta-lactamase


Mass: 44758.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. KCB13F003 (bacteria) / Gene: ulm16 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D3E317
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris hydrochloride pH 8.5, 200 mM Sodium acetate trihydrate, 30% w/v PEG4000

-
Data collection

DiffractionMean temperature: 273.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.058→50 Å / Num. obs: 43075 / % possible obs: 97.9 % / Redundancy: 3 % / CC1/2: 0.984 / CC star: 0.996 / Rpim(I) all: 0.065 / Rrim(I) all: 0.156 / Χ2: 0.092 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible allMean I/σ(I) obs
2.07-2.143.10.67643270.5050.8190.3280.7851.18498.3
2.14-2.233.10.57843340.4410.7820.2770.6671.14498.75.533
2.23-2.3330.44943560.7360.9210.2170.5191.12998.26.424
2.33-2.4530.37942720.7430.9230.1870.441.09597.66.971
2.45-2.612.90.30942541.18697.1
2.61-2.813.20.22643121.15998.5
2.81-3.093.10.17543541.11498.2
3.09-3.5430.11642931.06797.5
3.54-4.463.10.07943271.03398.3
4.46-5030.0642461.00496.3

-
Processing

Software
NameVersionClassification
PHENIX1.12refinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.058→32.8 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2215 1137 5.15 %
Rwork0.1796 --
obs0.1818 22089 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.058→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 0 195 3161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033060
X-RAY DIFFRACTIONf_angle_d0.6324193
X-RAY DIFFRACTIONf_dihedral_angle_d2.2192396
X-RAY DIFFRACTIONf_chiral_restr0.042468
X-RAY DIFFRACTIONf_plane_restr0.004566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0583-2.1520.2711280.22562564X-RAY DIFFRACTION97
2.152-2.26540.26761350.21652662X-RAY DIFFRACTION99
2.2654-2.40730.27181370.20812614X-RAY DIFFRACTION98
2.4073-2.59310.27281430.20862596X-RAY DIFFRACTION97
2.5931-2.8540.26591500.21052619X-RAY DIFFRACTION99
2.854-3.26660.26151430.19652615X-RAY DIFFRACTION98
3.2666-4.11430.18561590.15682640X-RAY DIFFRACTION99
4.1143-32.80.17241420.14652642X-RAY DIFFRACTION97
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)
11.6935-0.0459-0.61321.12331.86832.2633-0.10390.4474-0.0764-0.272-0.07130.6470.0346-0.1240.16510.3544-0.001-0.04580.25180.02540.45874.09583.9011-10.9628
22.26070.00280.06392.7061-2.20094.5735-0.0824-0.1782-0.22070.0385-0.1368-0.40330.09810.29120.24190.14120.01410.05430.1713-0.02040.386116.7147-1.50177.5071
34.50290.0957-0.03621.98110.78752.42090.0458-0.7563-0.2620.13310.0254-0.17580.18960.1123-0.03030.19030.02810.00930.3130.05490.284615.1035-1.199924.9911
42.6858-0.23510.64590.9497-0.54313.1514-0.0197-0.0196-0.2421-0.1142-0.0036-0.2206-0.02370.4831-0.10750.20160.03770.03360.22250.00070.370622.1546-1.02656.6531
53.49770.05631.0762.2807-0.29963.91540.13640.0697-0.6902-0.2232-0.0224-0.22030.20740.3944-0.06040.26010.01050.06570.235-0.0290.50396.8668-8.00196.5521
63.26081.372-0.08987.0374-0.78882.1822-0.09640.08420.1199-0.15960.16520.60060.0299-0.1764-0.04560.20130.0117-0.00730.18260.00850.33343.75423.1029-2.1549
71.4825-0.4252-0.93920.29150.05650.4842-0.2154-0.0767-0.21010.16420.0390.27590.3929-0.19580.30170.30340.03040.00210.3286-0.01040.4555-10.79325.852612.2086
87.1477-2.4422.05784.18730.68375.1841-0.1545-0.21440.45630.01550.0847-0.2536-0.2757-0.06650.03240.22150.00470.08150.2358-0.00830.4215-5.515711.093422.4871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 198 )
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 247 )
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 308 )
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 345 )
7X-RAY DIFFRACTION7chain 'A' and (resid 346 through 369 )
8X-RAY DIFFRACTION8chain 'A' and (resid 370 through 441 )

+
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