[English] 日本語
Yorodumi
- PDB-4plp: Crystal Structure of the Homospermidine Synthase (HSS) from Blast... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4plp
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / homospermidine synthase / oxidoreductase / rossman fold / NAD / putrescine
Function / homology
Function and homology information


homospermidine synthase (spermidine-specific) activity / homospermidine synthase / homospermidine synthase activity
Similarity search - Function
homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsKrossa, S.
CitationJournal: Sci Rep / Year: 2016
Title: Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism.
Authors: Krossa, S. / Faust, A. / Ober, D. / Scheidig, A.J.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Dec 20, 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: Homospermidine synthase
B: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3475
Polymers105,9612
Non-polymers1,3863
Water18,6461035
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.045, 109.792, 192.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Homospermidine synthase / HSS


Mass: 52980.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: hss / Plasmid: pETM14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32323, homospermidine synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-acetate, ammoniumacetate, PEG 3350, PEG400 as cryoprotectant

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 12, 2011
RadiationMonochromator: Si111 DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.314→96.478 Å / Num. all: 307932 / Num. obs: 307932 / % possible obs: 87.5 % / Redundancy: 3.5 % / Rpim(I) all: 0.112 / Rrim(I) all: 0.215 / Rsym value: 0.182 / Net I/av σ(I): 3.456 / Net I/σ(I): 4.5 / Num. measured all: 1068673
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.31-1.382.39.3357.3170.154142232675.6939.3357.31710.145.8
1.38-1.472.85.5654.540.298674347593.1555.5654.540.272.3
1.47-1.573.53.0422.580.3153898441121.5933.0422.580.497.3
1.57-1.73.71.8261.5660.5157161421020.9331.8261.5660.899.4
1.7-1.863.71.1540.9890.7144999388140.591.1540.9891.699.5
1.86-2.083.70.6040.5161.3131102352390.3110.6040.5163.499.6
2.08-2.43.70.3220.2752.4116723311680.1660.3220.2756.599.6
2.4-2.943.70.1480.1265.498024264210.0760.1480.12610.799.4
2.94-4.153.60.070.05911.373717204860.0360.070.05918.898.9
4.15-47.7133.50.0460.03914.840233115640.0240.0460.0392498.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å47.59 Å
Translation3 Å47.59 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
MOLREPphasing
ARPmodel building
PDB_EXTRACT3.11data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PH5

2ph5


Resolution: 1.49→9.996 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 11959 5.03 %
Rwork0.1906 225951 -
obs0.1924 237910 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.32 Å2 / Biso mean: 31.2906 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: LAST / Resolution: 1.49→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 92 1035 8541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127887
X-RAY DIFFRACTIONf_angle_d1.41310796
X-RAY DIFFRACTIONf_chiral_restr0.0811166
X-RAY DIFFRACTIONf_plane_restr0.0071420
X-RAY DIFFRACTIONf_dihedral_angle_d15.1342883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.50690.39883250.3966569689487
1.5069-1.52450.39633900.38497220761095
1.5245-1.54310.38824090.37077408781798
1.5431-1.56250.37763630.36657513787699
1.5625-1.5830.40414160.36047429784599
1.583-1.60460.37494140.35547502791699
1.6046-1.62740.33943950.33397554794999
1.6274-1.65160.37164010.33227474787599
1.6516-1.67730.34474070.33187494790199
1.6773-1.70470.33353860.33387522790899
1.7047-1.73390.34654100.32347521793199
1.7339-1.76530.33283940.30897571796599
1.7653-1.79910.34344240.29347580800499
1.7991-1.83560.323970.28387544794199
1.8356-1.87520.30294110.27967516792799
1.8752-1.91850.31633660.2817586795299
1.9185-1.96620.3023770.26677589796699
1.9662-2.01890.23354020.216175927994100
2.0189-2.07780.24764130.20637607802099
2.0778-2.14420.25294160.19375657981100
2.1442-2.22010.20614060.178375897995100
2.2201-2.30790.21664060.17177615802199
2.3079-2.41150.20074040.16247632803699
2.4115-2.53670.20764110.15387597800899
2.5367-2.69270.19074210.15167625804699
2.6927-2.8960.20213990.15147640803999
2.896-3.17880.16723820.15297675805799
3.1788-3.61960.18024140.14577620803499
3.6196-4.49040.1633840.12777710809498
4.4904-9.99640.16274160.13297892830898

+
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