[English] 日本語
Yorodumi
- PDB-6li4: Crystal structure of MCR-1-S -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6li4
TitleCrystal structure of MCR-1-S
ComponentsProbable phosphatidylethanolamine transferase Mcr-1
KeywordsTRANSFERASE / MCR-1 Zn(II) / ANTIBIOTIC
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / Transferases; Transferring phosphorus-containing groups / sulfuric ester hydrolase activity / response to antibiotic / plasma membrane
Similarity search - Function
Phosphoethanolamine transferase, N-terminal / Phosphoethanolamine transferase EptA/EptB / Phosphoethanolamine transferase / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
Probable phosphatidylethanolamine transferase Mcr-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, Q. / Wang, M. / Sun, H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17307017 Hong Kong
CitationJournal: Nat Commun / Year: 2020
Title: Resensitizing carbapenem- and colistin-resistant bacteria to antibiotics using auranofin.
Authors: Sun, H. / Zhang, Q. / Wang, R. / Wang, H. / Wong, Y.T. / Wang, M. / Hao, Q. / Yan, A. / Kao, R.Y. / Ho, P.L. / Li, H.
History
DepositionDec 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable phosphatidylethanolamine transferase Mcr-1
B: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5944
Polymers74,4632
Non-polymers1312
Water5,459303
1
A: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2972
Polymers37,2311
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable phosphatidylethanolamine transferase Mcr-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2972
Polymers37,2311
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.970, 84.180, 81.400
Angle α, β, γ (deg.)90.000, 98.760, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

#1: Protein Probable phosphatidylethanolamine transferase Mcr-1 / Polymyxin resistance protein MCR-1


Mass: 37231.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mcr1, mcr-1, APZ14_31440 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0R6L508, Transferases; Transferring phosphorus-containing groups
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100mM KSCN, 32% PEG 3350, 100mM Tris-HNO3, pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2018 / Details: Null
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.78→42.09 Å / Num. obs: 59043 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Net I/σ(I): 8.7 / Num. measured all: 389264 / Scaling rejects: 100
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.836.90.7612985343190.9170.310.8231.897.4
7.96-42.096.10.06742076890.9920.0290.0731897.8

-
Processing

Software
NameVersionClassification
PHENIXv1.15refinement
XDSBuild 20180808data reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GOV
Resolution: 1.78→37.29 Å / SU ML: 0.2307 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.4286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 2852 4.86 %
Rwork0.1914 55884 -
obs0.1933 58736 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.03 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 2 303 5310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00645119
X-RAY DIFFRACTIONf_angle_d0.83076975
X-RAY DIFFRACTIONf_chiral_restr0.0521780
X-RAY DIFFRACTIONf_plane_restr0.0051916
X-RAY DIFFRACTIONf_dihedral_angle_d18.58331819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.34021260.30312774X-RAY DIFFRACTION96.25
1.81-1.840.34151490.28762777X-RAY DIFFRACTION98.95
1.84-1.880.32521300.2692860X-RAY DIFFRACTION99.14
1.88-1.920.34171480.2512757X-RAY DIFFRACTION98.54
1.92-1.960.30241410.24842811X-RAY DIFFRACTION98.01
1.96-20.30581340.24322784X-RAY DIFFRACTION98.45
2-2.050.3211440.24722828X-RAY DIFFRACTION98.61
2.05-2.110.29621320.23552787X-RAY DIFFRACTION98.65
2.11-2.170.33021680.23512780X-RAY DIFFRACTION98.17
2.17-2.240.25151430.22312833X-RAY DIFFRACTION98.61
2.24-2.320.28991460.21832756X-RAY DIFFRACTION97.48
2.32-2.420.26231430.21792744X-RAY DIFFRACTION96.52
2.42-2.530.25071360.22372628X-RAY DIFFRACTION92.78
2.53-2.660.23031420.21662796X-RAY DIFFRACTION97.64
2.66-2.830.28341510.21132822X-RAY DIFFRACTION98.71
2.83-3.040.23451440.19632805X-RAY DIFFRACTION98.66
3.04-3.350.18761520.1812852X-RAY DIFFRACTION98.95
3.35-3.830.22551480.16852800X-RAY DIFFRACTION98.17
3.83-4.830.17421310.14142800X-RAY DIFFRACTION96.83
4.83-37.290.16691440.15952890X-RAY DIFFRACTION98.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.737987631237-0.6992294044630.1381662677971.162638609660.3062121000191.41239950011-0.02837748112920.1058134253690.0293842542477-0.2026379406660.03057549597820.14392465942-0.09879503765640.0377782716715-0.01738802857420.270405539819-0.0397988051427-0.04764133722030.2458700127590.003191237251720.2483677503774.801305647561.440701949173.47095731982
21.05430621003-0.3602661560330.2285720399491.163921789790.3093335424591.87891125156-0.1200686517740.04577359507760.242779287862-0.1107722500270.0845459061989-0.0715959484642-0.4984081479690.1849884310920.06056006799740.34763634709-0.0495349985808-0.03984316096570.241555837256-0.0009752984932210.3008959150428.5640354121313.204392234410.251930335
32.93574260167-1.660047027540.6396985066711.96343384881-0.6648940119341.15209026566-0.197642965867-0.2046648596750.355229124490.1598822514770.195908667331-0.02902009904530.0295580562838-0.305029969154-0.006736461376830.2575786920680.0108096882086-0.01158232330320.351156152632-0.01255082521570.3247228494363.915971232021.2915100003422.9535629796
41.25799511656-0.6556617524370.8351096168231.81297595736-0.3278053919021.49803532656-0.1193919362490.01444068677020.02312044876860.06957672404010.1130799387550.0300636982661-0.0414916934731-0.06501794980590.02748510598880.225490750676-0.01722797139350.005596940685470.257655923124-0.01112039879120.2003766073798.71312713409-1.0524913773115.6381694865
52.9801911530.383509175192-1.10055642552.28202222144-0.3541257181572.67474150579-0.263906036994-0.137880261334-0.02661082731230.4535960407290.381824825657-0.4240951037230.5465538722050.504353787353-0.01987015305220.4740420226360.10849899876-0.09062427168720.417391946937-0.03755930166390.37068611746422.9212096547-15.965319228316.4839719064
60.706249250376-0.1850336227070.5317455628671.15860319133-0.07124075235281.60016653969-0.0579183641028-0.0126931790994-0.0352523134218-0.05280281686050.07141331993910.08711361373810.166707445642-0.0224624081786-0.02555054981540.25985076806-0.032099540414-0.03518527894910.262329341095-0.00648714393850.2606368586398.99299939672-5.742766023539.7799608074
75.168635428140.488967923059-0.5770606589351.75412599188-0.09907392204811.70981635185-0.194715007880.2897481947240.219148702608-0.2080622334590.1161280814990.1066985620240.0757473160683-0.09049849401270.1265192335620.285004779334-0.0527549184628-0.04424684061880.296688556074-0.003498968864580.2162583657057.83921150373-2.879397515520.592705883114
81.34040355988-0.694455984712-0.2628935459691.367318755050.4274998744710.90818019283-0.0373381624630.1924660078450.00298866318838-0.2437817293270.01778013108630.329467039944-0.289206717591-0.168687645697-0.0004536352185270.444976510631-0.00807545103306-0.110437230230.285668682880.01913486510410.2929640315210.3922533797115.51809368279-5.27243424382
91.368278027860.0231664228725-0.4016552208840.3178031546630.3642882214260.5283240616520.19928660372-0.471193714818-0.4038735651150.187736166243-0.3081282793830.2031656122080.220522684811-0.5246523029860.0260907130720.344485654946-0.204781526476-0.005947110369150.6514142439810.05020528413560.357715077151-10.506008504715.994218499347.9344899221
101.113516417920.349446198970.2725674003590.804898194288-0.1093549004381.074611673390.0878774251193-0.11962360105-0.0767304324671-0.1048339360630.009089474782150.05967640002310.079223489652-0.13856396842-0.07303960804090.2321857389360.0116858337113-0.01132344480860.329224484322-0.04104856247270.2325674944635.5804243998124.605111592530.411914827
111.74464631149-0.3348709742950.02883326357951.45138100809-0.08649070931831.458080999120.165493211862-0.2194969356870.157418464229-0.0122333862729-0.0391558089690.280700771291-0.146645391497-0.705051005757-0.0559677046160.262822214618-0.01168222360860.008844021264020.684621127319-0.03902229314930.400591438343-15.804220227625.561073962339.5953067861
121.314179325740.6181565580.3342947205390.7071983533890.17936540170.9727362427550.14058603435-0.4893566833310.1645340709180.195795074942-0.1784044702510.163565166596-0.0714755878544-0.4424519161780.02727988835220.282551837559-0.03098484992250.02941845342880.529089807839-0.06371804650570.2736717424951.5836825673332.739299628749.1509840309
131.669922433391.20580845169-0.6004339886842.23862153243-1.147153142152.133780340520.172134690181-0.265382686014-0.09499854886760.382086024948-0.01310246918370.0461480630062-0.0728354974642-0.37501555498-0.09390430501860.206546161426-0.0413983442098-0.009501643018110.362781575894-0.006804569107860.2336448100741.2857999700827.344530499445.1086451033
141.830823266650.178543172953-0.6095437870661.375594831760.4415478737751.77562954442-0.0319355425550.09566795954840.379592771238-0.3885323972760.0558726853288-0.0828135077414-0.392355815070.2895036545830.03563991670580.306821211416-0.04474476039490.02007314410730.3296077746020.01255641958270.30797825143115.678257372940.272635562331.1807957194
151.283088688920.4817652241380.3948907033810.8097188959080.2883957549621.253497356890.128044452619-0.0183054283727-0.103410395140.0301589545819-0.05456071835370.1142311060330.106238456878-0.0801797779495-0.04254338077030.22387080589-0.0003307912489460.004004509202810.333611284034-0.002412219215720.2428749176833.8532115041523.907702603433.8238654526
162.898060274320.577605667878-0.1129678152870.157677274871-0.2668446076741.606840247940.0103526283481-0.147301599982-0.4530334480920.0409771952159-0.1407422242620.3845101122970.514431969506-0.70048205993-0.03338616255570.41849798403-0.135355604433-0.0161192889130.501814270866-0.01026976804330.492303013072-9.8042821249111.790619755937.7178673026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 217 through 293 )
2X-RAY DIFFRACTION2chain 'A' and (resid 294 through 356 )
3X-RAY DIFFRACTION3chain 'A' and (resid 357 through 380 )
4X-RAY DIFFRACTION4chain 'A' and (resid 381 through 407 )
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 423 )
6X-RAY DIFFRACTION6chain 'A' and (resid 424 through 481 )
7X-RAY DIFFRACTION7chain 'A' and (resid 482 through 502 )
8X-RAY DIFFRACTION8chain 'A' and (resid 503 through 541 )
9X-RAY DIFFRACTION9chain 'B' and (resid 216 through 245 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 292 )
11X-RAY DIFFRACTION11chain 'B' and (resid 293 through 318 )
12X-RAY DIFFRACTION12chain 'B' and (resid 319 through 379 )
13X-RAY DIFFRACTION13chain 'B' and (resid 380 through 398 )
14X-RAY DIFFRACTION14chain 'B' and (resid 399 through 423 )
15X-RAY DIFFRACTION15chain 'B' and (resid 424 through 525 )
16X-RAY DIFFRACTION16chain 'B' and (resid 526 through 541 )

+
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