[English] 日本語
Yorodumi
- PDB-9qlk: Structure of piperazate synthase from Streptomyces sp. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9qlk
TitleStructure of piperazate synthase from Streptomyces sp.
ComponentsFMN-binding negative transcriptional regulator
KeywordsLYASE / Piperazate synthase / piperazic acid / N-N bond formation / heme-binding
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sp. B93 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsPal, N. / Schroder, S. / Sagmeister, T. / Daniel, B. / Gruber, K.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission101073065European Union
CitationJournal: To Be Published
Title: Structure of piperazate synthase from Streptomyces sp.
Authors: Pal, N. / Schroder, S. / Daniel, B. / Gruber, K.
History
DepositionMar 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FMN-binding negative transcriptional regulator
B: FMN-binding negative transcriptional regulator
C: FMN-binding negative transcriptional regulator
D: FMN-binding negative transcriptional regulator
E: FMN-binding negative transcriptional regulator
F: FMN-binding negative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,10521
Polymers153,7196
Non-polymers4,38615
Water6,089338
1
A: FMN-binding negative transcriptional regulator
B: FMN-binding negative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6056
Polymers51,2402
Non-polymers1,3654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-95 kcal/mol
Surface area17220 Å2
MethodPISA
2
C: FMN-binding negative transcriptional regulator
D: FMN-binding negative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,92110
Polymers51,2402
Non-polymers1,6828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8570 Å2
ΔGint-104 kcal/mol
Surface area17410 Å2
MethodPISA
3
E: FMN-binding negative transcriptional regulator
F: FMN-binding negative transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5795
Polymers51,2402
Non-polymers1,3393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-81 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.708, 141.708, 57.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
FMN-binding negative transcriptional regulator


Mass: 25619.816 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. B93 (bacteria) / Strain: B93 / Gene: KBY47_09630 / Plasmid: pET28a / Details (production host): C-terminal His-Tag / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo21 (DE3)

-
Non-polymers , 5 types, 353 molecules

#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 % / Description: brown needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M Ca acetate, 0.08 M Na cacodylate, 14.4% PEG 8000, 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 14, 2025
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.14→51.79 Å / Num. obs: 78184 / % possible obs: 99.95 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.01 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.069 / Rrim(I) all: 0.1596 / Rsym value: 0.1437 / Net I/σ(I): 7
Reflection shellResolution: 2.14→2.17 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3163 / CC1/2: 0.382 / CC star: 0.743 / Rpim(I) all: 0.6121 / Rrim(I) all: 1.428 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimless0.7.15data scaling
Coot0.9.8.93model building
MOLREP11.9.02phasing
XDS20250430data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→51.79 Å / SU ML: 0.3369 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.517
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2652 3541 5.01 %
Rwork0.1926 67197 -
obs0.1962 70738 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.34 Å2
Refinement stepCycle: LAST / Resolution: 2.14→51.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9909 0 353 338 10600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012810626
X-RAY DIFFRACTIONf_angle_d1.194714548
X-RAY DIFFRACTIONf_chiral_restr0.05981498
X-RAY DIFFRACTIONf_plane_restr0.01411906
X-RAY DIFFRACTIONf_dihedral_angle_d15.46653849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.170.30861560.27842666X-RAY DIFFRACTION100
2.17-2.20.32271600.26122671X-RAY DIFFRACTION100
2.2-2.230.33971700.25832638X-RAY DIFFRACTION100
2.23-2.270.33921360.26612722X-RAY DIFFRACTION99.93
2.27-2.310.30251440.27542675X-RAY DIFFRACTION99.96
2.31-2.340.32241780.26812641X-RAY DIFFRACTION99.93
2.35-2.390.33951660.2462707X-RAY DIFFRACTION100
2.39-2.430.32591620.25812645X-RAY DIFFRACTION100
2.43-2.480.32351420.24762740X-RAY DIFFRACTION99.93
2.48-2.540.31011240.24422639X-RAY DIFFRACTION99.96
2.54-2.60.30451020.24922793X-RAY DIFFRACTION100
2.6-2.660.3325760.25342685X-RAY DIFFRACTION99.96
2.66-2.730.3081340.23462724X-RAY DIFFRACTION100
2.73-2.810.33251120.21752707X-RAY DIFFRACTION100
2.81-2.90.33661640.22082666X-RAY DIFFRACTION100
2.9-3.010.28561350.22052743X-RAY DIFFRACTION99.97
3.01-3.130.26041260.21142650X-RAY DIFFRACTION100
3.13-3.270.28221460.19752697X-RAY DIFFRACTION99.96
3.27-3.440.2961320.1892689X-RAY DIFFRACTION99.86
3.44-3.660.27671180.17282718X-RAY DIFFRACTION99.96
3.66-3.940.25521580.15912670X-RAY DIFFRACTION99.96
3.94-4.340.21581480.14372700X-RAY DIFFRACTION100
4.34-4.960.1842100.13912591X-RAY DIFFRACTION99.93
4.97-6.250.24251320.15752718X-RAY DIFFRACTION100
6.26-51.790.22121100.15932702X-RAY DIFFRACTION99.36

+
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