[English] 日本語
Yorodumi
- PDB-9v4g: Prenyltransferase Ord1 wild type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9v4g
TitlePrenyltransferase Ord1 wild type
Componentsprenyltransferase
KeywordsTRANSFERASE / Prenyltransferase
Biological speciesStreptomyces sp. KS84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOshiro, T. / Uehara, S. / Ito, T. / Tanaka, Y. / Kodera, Y. / Matsui, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17KK0141 Japan
Japan Society for the Promotion of Science (JSPS)21K06036 Japan
CitationJournal: Biochemistry / Year: 2025
Title: Structure-Activity Relationship of an All-alpha-helical Prenyltransferase Reveals the Mechanism of Indole Prenylation.
Authors: Oshiro, T. / Uehara, S. / Suto, A. / Tanaka, Y. / Ito, T. / Kodera, Y. / Matsui, T.
History
DepositionMay 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: prenyltransferase
C: prenyltransferase
D: prenyltransferase
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38012
Polymers144,7814
Non-polymers5998
Water3,117173
1
A: prenyltransferase
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7076
Polymers72,3912
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6736
Polymers72,3912
Non-polymers2824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.000, 72.210, 84.190
Angle α, β, γ (deg.)86.040, 69.500, 90.020
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 90 or resid 97 through 330))
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 44 through 224 or resid 240 through 328))
d_2ens_2(chain "D" and (resid 44 through 90 or resid 104...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNCYSCYSAA8 - 908 - 90
d_12ens_1LYSLYSLEULEUAA97 - 33097 - 330
d_21ens_1GLNGLNLEULEUCB8 - 3308 - 330
d_11ens_2PHEPHETYRTYRBD44 - 22444 - 224
d_12ens_2GLYGLYLEULEUBD240 - 328240 - 328
d_21ens_2PHEPHECYSCYSDC44 - 9044 - 90
d_22ens_2PHEPHETYRTYRDC104 - 224104 - 224
d_23ens_2GLYGLYALAALADC226 - 266226 - 266
d_24ens_2ALAALAARGARGDC273 - 275273 - 275
d_25ens_2LYSLYSLEULEUDC277 - 328277 - 328

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99997968608225, -0.00096702332452842, 0.0063001816429663), (-0.00096430197164901, -0.99999944046052, -0.00043497167191598), (0.0063005987455182, 0.00042888755835716, -0.99998005905663)0.57187657639924, -39.271909935581, -92.772870236911
2given(0.99747701070139, 0.070572669376789, 0.0076883977039424), (0.0705695394455, -0.99750663178962, 0.000677966199635), (0.0077170735819742, -0.00013368901312744, -0.99997021400769)2.0990144419089, -36.651776024055, -92.326056465626

-
Components

#1: Protein
prenyltransferase


Mass: 36195.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DDBJ LC876682 / Source: (gene. exp.) Streptomyces sp. KS84 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris,pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.045 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 74272 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.58
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 11833 / CC1/2: 0.774 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX1.19.2.4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial phase from Se-SAD model

Resolution: 2.1→44.4 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.0116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 3795 5.12 %
Rwork0.2287 70359 -
obs0.2324 74154 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8506 0 35 173 8714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00378676
X-RAY DIFFRACTIONf_angle_d0.675311748
X-RAY DIFFRACTIONf_chiral_restr0.03981332
X-RAY DIFFRACTIONf_plane_restr0.00571550
X-RAY DIFFRACTIONf_dihedral_angle_d13.81643173
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.4381033974965
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.3339470374973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.29981760.30543343X-RAY DIFFRACTION88.96
2.13-2.170.28831860.29263534X-RAY DIFFRACTION92.15
2.17-2.210.31421840.29793502X-RAY DIFFRACTION92.28
2.21-2.260.27991880.28693564X-RAY DIFFRACTION92.43
2.26-2.310.31161800.28193435X-RAY DIFFRACTION92.56
2.31-2.360.30421890.27963580X-RAY DIFFRACTION92.6
2.36-2.420.26851850.26753509X-RAY DIFFRACTION92.76
2.42-2.490.27131860.26993549X-RAY DIFFRACTION92.71
2.49-2.560.27481860.25713520X-RAY DIFFRACTION92.9
2.56-2.640.26691840.2553505X-RAY DIFFRACTION93.17
2.64-2.740.29851880.26283578X-RAY DIFFRACTION93.13
2.74-2.850.27671850.24573514X-RAY DIFFRACTION93.23
2.85-2.980.29411870.24783542X-RAY DIFFRACTION93.21
2.98-3.130.2811890.25623590X-RAY DIFFRACTION93.47
3.13-3.330.25311840.24343501X-RAY DIFFRACTION93.36
3.33-3.590.27871890.22483581X-RAY DIFFRACTION93.43
3.59-3.950.21491850.20993532X-RAY DIFFRACTION92.7
3.95-4.520.21371860.18443531X-RAY DIFFRACTION93.26
4.52-5.690.21011860.20683530X-RAY DIFFRACTION93.07
5.69-44.40.2181850.20733506X-RAY DIFFRACTION91.95
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)
10.39130186143458-0.29173707857172-0.0388944265972641.207922170986-0.284161428872490.42832971636640.050007888304569-0.0160307593863050.18560506239097-0.028780705973109-0.000111009907976820.17215578004827-0.020669912783647-0.0651286578656240.000307777165309620.29670361093029-6.5700882608287E-6-0.00620994847389060.41525497555380.0520098266624590.32199564974716-31.007058620554-6.0428455639027-78.79376463537
20.030703418963335-0.0119452346952670.330218616504011.153375024426-0.0157682316764751.96093454561090.16790951367695-0.1736212646452-0.13376076739490.19598316643228-0.13887847733480.16092012801380.584656980383180.12976315605689-0.000494891168324270.52697293856455-0.010018164364329-0.00966611746076520.572081624297470.135600996885150.34109329497631-25.840358865058-32.738598763987-54.718770273487
3-0.0385113149211040.54936661170795-0.0956819509423591.0717338555573-0.425928694841450.7559778099485-0.0546438910737580.10387280010394-0.13877989685811-0.0200480569976160.124827229489510.181121007089550.10657184471452-0.192481543690640.000843824359366790.28416678544837-0.0116334861609870.0076891635436580.422775146459380.0711547616087480.39021385096902-31.305002754713-35.599149306714-15.42182326993
40.28041806465575-0.13211067950864-0.071114967527190.328476787198190.128837351509251.45858320443270.0598362599161490.234340011964550.22430161662132-0.069904938302804-0.0536046421985050.11533008252802-0.32253663825320.023798195336043-0.000305281786281860.46241342804528-0.00356717567636180.00165892857719360.665900665907820.15793970791790.38384510968211-27.084507106076-5.6903672680097-37.272195349617
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 5:403)AA5 - 3301 - 313
22(chain B and resseq 8:406)BD39 - 3341 - 262
33(chain C and resseq 44:330)CB44 - 33037 - 304
44(chain D and resseq 39:403)DC44 - 3281 - 259

+
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