[English] 日本語
Yorodumi
- PDB-8ahd: The apo structure of the Corramycin phosphotransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ahd
TitleThe apo structure of the Corramycin phosphotransferase
ComponentsCorramycin phosphotransferase
KeywordsTRANSFERASE / Phosphotransferase / Complex / Resistance protein
Function / homologyAminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Alpha-Beta Complex / Alpha Beta
Function and homology information
Biological speciesCorallococcus coralloides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAdam, S. / Mueller, R. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: The apo structure of the Corramycin phosphotransferase
Authors: Adam, S. / Mueller, R. / Koehnke, J.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Corramycin phosphotransferase
B: Corramycin phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6874
Polymers82,5032
Non-polymers1842
Water7,494416
1
A: Corramycin phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3442
Polymers41,2511
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Corramycin phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3442
Polymers41,2511
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.088, 69.863, 117.536
Angle α, β, γ (deg.)90.000, 98.110, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 33 or resid 40 through 56 or resid 66 through 364 or resid 401))
d_2ens_1(chain "B" and (resid 14 through 364 or resid 401))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROLEULEUAA14 - 3314 - 33
d_12ALAALAPHEPHEAA39 - 5739 - 57
d_13GLYGLYPROPROAA66 - 36466 - 364
d_14GOLGOLGOLGOLAC401
d_21VALVALPROPROBB13 - 36413 - 364
d_22GOLGOLGOLGOLBD401

-
Components

#1: Protein Corramycin phosphotransferase / ComG / Aminoglycoside phosphotransferase family protein


Mass: 41251.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ST201330 (DSM24989) / Source: (gene. exp.) Corallococcus coralloides (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Magnesium chloride, Tris, PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→116.4 Å / Num. obs: 45561 / % possible obs: 97.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 6647

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→59.9 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.3627
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 2155 4.74 %
Rwork0.2081 43273 -
obs0.2109 45428 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→59.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 12 416 5811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01155536
X-RAY DIFFRACTIONf_angle_d1.21037500
X-RAY DIFFRACTIONf_chiral_restr0.0551790
X-RAY DIFFRACTIONf_plane_restr0.0178983
X-RAY DIFFRACTIONf_dihedral_angle_d6.2296773
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.616562983324 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.31921690.25852860X-RAY DIFFRACTION97.68
2.15-2.20.29291540.25372879X-RAY DIFFRACTION97.62
2.2-2.260.36091430.28092903X-RAY DIFFRACTION97.1
2.26-2.330.35721420.2482878X-RAY DIFFRACTION97.26
2.33-2.40.28191330.22332894X-RAY DIFFRACTION97.21
2.4-2.490.25151410.20752863X-RAY DIFFRACTION96.16
2.49-2.590.26491460.19712792X-RAY DIFFRACTION94.41
2.59-2.710.25651340.20562923X-RAY DIFFRACTION97.98
2.71-2.850.24321720.21012904X-RAY DIFFRACTION97.93
2.85-3.030.23081200.20862938X-RAY DIFFRACTION97.54
3.03-3.260.2681380.21462831X-RAY DIFFRACTION94.86
3.26-3.590.2991460.19142920X-RAY DIFFRACTION96.6
3.59-4.110.21821420.18212919X-RAY DIFFRACTION97.45
4.11-5.180.22871290.17422850X-RAY DIFFRACTION94.6
5.18-59.90.28741460.21522919X-RAY DIFFRACTION94.31
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)
14.0936012421-2.76575622798-3.021476663574.986742775272.744150536738.02410664971-0.04731789488190.1952798906290.466666167756-0.5275276547490.103016801827-0.482298890262-0.6384975921550.776490802073-0.1180934101770.308016526676-0.0866553247616-0.01030528736360.342928853610.03037901024190.2358980253716.74886382753.8843040606100.341913858
22.034112931532.23804410252-0.5159770717153.02102808325-0.618821947722.21900440737-0.1829146699050.2812012029650.143293027807-0.1480073859420.129785131695-0.20617455089-0.1330011474120.06253878933970.011868169160.209680015192-0.009752678114010.01004775749070.167851782798-0.02675049817260.2754901624729.2223369843349.247429006105.531944832
34.216379070634.01750781953-4.247960002278.26732731415-3.778917808494.296020971450.08034529484040.2968542761490.4091029679730.1414735561770.1162170705310.447215743092-0.276385042959-0.150946175088-0.154973455280.121233883949-0.0286936683264-0.04802255000770.257357059333-0.007610715892180.3533218074612.3196810205351.4684865807110.147470398
42.790643642962.73655518581-0.07868458610176.36478582322-0.3168187361810.531804697858-0.0179471245144-0.208590053797-0.149391720291-0.165442531419-0.143044024843-0.1795887800260.1062116789340.1564426611020.1860658322890.1733904013550.03469837265990.03136460107710.2032992912220.02980426576560.3179298294559.5704212418834.3951515207108.211641647
56.17012634136-4.89320976158-0.09297565271514.425270126050.5951580697840.602384414342-0.0172941769527-0.1911920900840.06676414676630.154908158260.00323529629838-0.107842079651-0.02301726489710.03683676981520.03848455419370.148847685513-0.03237669595790.03303583901770.1342779880920.01778491780920.196291275616-3.6913285091534.0902629013117.767353987
62.644501913593.22469561873.444814315246.397450873976.152748110116.36749194077-0.2165438229860.02173993008380.162525674294-0.63871014502-0.02379498238240.602859763602-0.633362499477-0.05018245567120.2479339966290.2747647051180.0300907492421-0.04399310754060.1668095839170.04015969620470.273203545422-19.039710327838.591552575297.906744855
72.041667563521.677996454931.124569302051.997453255511.094033610081.564501734530.004353351810220.0696552481303-0.0421654962154-0.155270654486-0.07245895302360.08881698999410.0120722615602-0.07672428653730.06797986194060.1789720693740.0167716575687-0.002203615467730.133031804574-0.001361509520660.214705453671-11.038431759133.0961686723106.379946855
82.333931140080.545931533747-1.262297868053.7951148663.274026802914.72967669854-0.130701210917-0.165475561493-0.2954191653280.2527501315570.02337816232890.3725291429050.2629018851580.185649297750.1220177314680.1685571204740.02327484955450.02257589778260.1567536130280.06039122364640.308846197672-10.426802352428.0367691656119.934090479
91.12591735314-0.346623637916-1.154993779042.608857853361.128788003835.982652112620.0258352042018-0.004671496954480.130260135317-0.247133163577-0.0711111192358-0.103762311069-0.2000859845690.4847936250450.04384735730490.161654829081-0.00574815114805-0.04076263663340.203055641420.01390887519590.288128751715-11.589660567123.318978897799.4563784881
103.900542585290.7961776215322.250515246351.091161797110.3923838841521.437881494560.385809284270.410622273534-0.530237836903-0.287116139248-0.00326335745721-0.3768825404540.2305600571440.188131996983-0.3426944280570.3605349210080.037816240843-0.006642346674090.178554996468-0.03067071814690.300389017764-11.589970324715.184494084598.1535560989
112.29250710432-3.785515662863.643982363646.52245524198-5.739521671996.07577642631-0.572438679646-1.70787759276-0.4840626501051.176297044430.0886962461848-0.323296099136-0.826063685454-0.3069292081690.48983159170.5875692585460.268553593201-0.298008030090.8724140215750.07329571580890.710088297014-3.4768411079510.1070741455104.671705308
125.59625457784-1.81782675675-1.131774596082.45099236750.3706966233371.98392483964-0.305174342673-0.6175328225850.3984252267060.3349495796910.239181485153-0.250630056791-0.1537310595490.0194844065910.05925594616860.2594193965210.0687808897886-0.05229565950940.2734665301030.01035920211570.221664953844-9.4830828460137.173397007569.1739640824
130.868197145326-0.2733323609160.4593981328821.5012067048-0.4000655905821.07607010196-0.0828521443789-0.07436243913020.08372768239210.07406468847110.0419461912553-0.0145951438869-0.0170252690873-0.06450411540860.05003045150230.1309048580840.000858439878970.02051151329110.183382476898-0.0105982350490.2207391925018.8860043134419.20089551265.8228237959
143.710653938620.570365257886-1.7116174971.79494803679-0.2995124054784.59383139721-0.140894094784-0.182110834005-0.1507302856830.2524843682010.1131408740730.08503254825250.240843302998-0.1938999036180.03203150220250.221533776220.0391857545273-0.02244624096870.162526775928-0.007841791523550.25551334096511.43374999235.5926368677175.3285572885
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 39 )AA14 - 391 - 21
22chain 'A' and (resid 40 through 73 )AA40 - 7322 - 47
33chain 'A' and (resid 74 through 93 )AA74 - 9348 - 67
44chain 'A' and (resid 94 through 113 )AA94 - 11368 - 87
55chain 'A' and (resid 114 through 141 )AA114 - 14188 - 115
66chain 'A' and (resid 142 through 170 )AA142 - 170116 - 144
77chain 'A' and (resid 171 through 243 )AA171 - 243145 - 217
88chain 'A' and (resid 244 through 267 )AA244 - 267218 - 241
99chain 'A' and (resid 268 through 325 )AA268 - 325242 - 299
1010chain 'A' and (resid 326 through 361 )AA326 - 361300 - 335
1111chain 'A' and (resid 362 through 364 )AA362 - 364336 - 338
1212chain 'B' and (resid 13 through 93 )BC13 - 931 - 66
1313chain 'B' and (resid 94 through 267 )BC94 - 26767 - 240
1414chain 'B' and (resid 268 through 364 )BC268 - 364241 - 337

+
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