[English] 日本語
Yorodumi
- PDB-22tz: Crystal structure of AstC in complex with farnesyl pyrophosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 22tz
TitleCrystal structure of AstC in complex with farnesyl pyrophosphate
ComponentsAstC
KeywordsBIOSYNTHETIC PROTEIN / Haloacid dehalogenase-like terpene cyclase
Function / homologyFARNESYL DIPHOSPHATE
Function and homology information
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsChen, T.-H. / Huang, K.-F. / Ko, T.-P. / Lin, H.-C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-109-L09 and AS-IV-114-L05 Taiwan
Ministry of Science and Technology (MoST, Taiwan)NSTC-111-2113-M-001-037-MY3 and NSTC-113-2628-M-001-014 Taiwan
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Dimerization-Dependent Trans-Domain Coupling Enables Intermediate Transfer in Fungal Haloacid Dehalogenase-Like Terpene Cyclases.
Authors: Chen, T.H. / Huang, K.F. / Chou, T.H. / Tseng, C.C. / Huang, R.J. / Ko, T.P. / Liang, S.Y. / Chein, R.J. / Lin, H.C.
History
DepositionJan 23, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AstC
B: AstC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3355
Polymers111,3322
Non-polymers1,0033
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-32 kcal/mol
Surface area36570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.872, 104.205, 127.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and resid 6 through 473)
d_2ens_1(chain "B" and resid 6 through 473)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 6 - 473 / Label seq-ID: 19 - 486

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.212821373801, -0.94841335859, -0.234987582867), (-0.948644302341, 0.142951905224, 0.282203367145), (-0.234053520565, 0.282978539895, -0.930130149748)Vector: 62. ...NCS oper: (Code: given
Matrix: (-0.212821373801, -0.94841335859, -0.234987582867), (-0.948644302341, 0.142951905224, 0.282203367145), (-0.234053520565, 0.282978539895, -0.930130149748)
Vector: 62.6321222097, 34.7750331925, 69.1933926785)

-
Components

#1: Protein AstC


Mass: 55665.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 4000, 100mM HEPES pH 7.5, 10% (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 14, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→30.03 Å / Num. obs: 25641 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 57.22 Å2 / Rmerge(I) obs: 0.263 / Net I/σ(I): 8.3
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.581 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2507 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.96→30.03 Å / SU ML: 0.3585 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 1152 5.01 %
Rwork0.1717 21860 -
obs0.1745 23012 89.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.92 Å2
Refinement stepCycle: LAST / Resolution: 2.96→30.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7483 0 63 228 7774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257712
X-RAY DIFFRACTIONf_angle_d0.590110453
X-RAY DIFFRACTIONf_chiral_restr0.04041181
X-RAY DIFFRACTIONf_plane_restr0.00761325
X-RAY DIFFRACTIONf_dihedral_angle_d15.55422840
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.962369988309 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.96-3.090.3464860.24631545X-RAY DIFFRACTION51.89
3.09-3.250.28531080.23322256X-RAY DIFFRACTION74.39
3.25-3.460.26131310.21132737X-RAY DIFFRACTION91.19
3.46-3.720.24981500.18713014X-RAY DIFFRACTION99.47
3.72-4.10.21631760.15793005X-RAY DIFFRACTION99.94
4.1-4.690.18051620.13413038X-RAY DIFFRACTION99.91
4.69-5.90.21451590.163062X-RAY DIFFRACTION99.85
5.9-30.030.23871800.17243203X-RAY DIFFRACTION99.88
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)
10.810923539657-0.277938681212-0.5304414055831.41989367746-0.1948172975641.54108051438-0.3581703900730.411833393831-0.0214227214654-0.796695013928-0.115700514887-0.3784156381020.6040161402290.00754175474713-0.004809629491420.999530225344-0.1039033113450.2516022618770.587374398172-0.02432688503320.72163609026843.697561032233.201387634412.8681896194
20.6244736546290.215375033695-0.4741522299521.58713197024-0.1494623834561.32021140128-0.4082991141510.7686162419580.011260864613-0.5676984461320.280522622553-0.2519169130550.107779193183-0.3517004815256.83765845948E-60.81992043627-0.1275307969890.05154243069320.9292660839240.02032124853170.4621865962526.731219901437.674990222510.504105657
32.228623255940.605645208404-0.5076901614141.93446593384-0.02902899876682.12826683367-0.1815561072860.346238895068-0.106340174253-0.210829367710.2387261140180.09352725855690.111067567414-0.03002977904680.0001125037944620.363845782974-0.0682003768863-0.02032151035380.536851610015-0.05633667898250.370454765613-0.16424968820619.240468593138.5891404039
41.22302039743-0.3650106219510.8998033774530.614685675786-0.1496688220061.67819478333-0.02788366910130.20095900979-0.3868292155050.0850870616757-0.0462667239553-0.03528776154140.3960376034890.189163491279-3.33415643703E-50.5166474256640.01651952277730.06513783703120.514166076529-0.1075572715460.72338249081519.63669869473.2940229165659.4938428682
50.7865457492420.188423798238-0.4091114120450.703433042166-0.6498600569480.7054855260850.000586119775783-0.0527380341175-0.1128876751780.2846771159910.003311191805140.00262000660152-0.05733344637240.02531162048186.41490036606E-60.431119287660.0158250755770.01877670970890.465135978537-0.09633026777230.45814970176917.412676432621.730783071461.8845213003
61.723978029850.180384724973-0.0334920520212.22019846618-1.431457646172.96850368799-0.1397429056530.07519425381870.0957852149007-0.08019326654040.0294708590323-0.26780545054-0.400964304684-0.154857761614-0.0009110526298210.4772092415740.00300494751607-0.01956324838630.332264890758-0.02904354558090.47851579475935.333558079348.527613541238.8709815737
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 98 )AA6 - 981 - 93
22chain 'A' and (resid 99 through 212 )AA99 - 21294 - 207
33chain 'A' and (resid 213 through 473 )AA213 - 473208 - 468
44chain 'B' and (resid 6 through 129 )BC6 - 1291 - 124
55chain 'B' and (resid 130 through 212 )BC130 - 212125 - 207
66chain 'B' and (resid 213 through 474 )BC213 - 474208 - 469

+
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