[English] 日本語
Yorodumi
- PDB-3flu: Crystal structure of dihydrodipicolinate synthase from the pathog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3flu
TitleCrystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / TIM barrel / beta-alpha-barrel / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Lysine biosynthesis / Schiff base
Function / homology
Function and homology information


4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel ...4-hydroxy-tetrahydrodipicolinate synthase, DapA / Schiff base-forming aldolase, conserved site / Dihydrodipicolinate synthase signature 1. / Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDevenish, S.R.A. / Hadfield, A.T.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis.
Authors: Devenish, S.R.A. / Huisman, F.H.A. / Parker, E.J. / Hadfield, A.T. / Gerrard, J.A.
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
C: Dihydrodipicolinate synthase
D: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,56051
Polymers126,1604
Non-polymers4,40047
Water16,898938
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-381 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.667, 115.684, 132.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31B
41C

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNMETMETDD3 - 139 - 19
21GLNGLNMETMETAA3 - 139 - 19
31GLNGLNMETMETBB3 - 139 - 19
41GLNGLNMETMETCC3 - 139 - 19
12ILEILEVALVALDD28 - 6334 - 69
22ILEILEVALVALAA28 - 6334 - 69
32ILEILEVALVALBB28 - 6334 - 69
42ILEILEVALVALCC28 - 6334 - 69
13VALVALTHRTHRDD67 - 8273 - 88
23VALVALTHRTHRAA67 - 8273 - 88
33VALVALTHRTHRBB67 - 8273 - 88
43VALVALTHRTHRCC67 - 8273 - 88
14ILEILETHRTHRDD86 - 14492 - 150
24ILEILETHRTHRAA86 - 14492 - 150
34ILEILETHRTHRBB86 - 14492 - 150
44ILEILETHRTHRCC86 - 14492 - 150
15PROPROILEILEDD155 - 174161 - 180
25PROPROILEILEAA155 - 174161 - 180
35PROPROILEILEBB155 - 174161 - 180
45PROPROILEILECC155 - 174161 - 180
16PHEPHELEULEUDD181 - 228187 - 234
26PHEPHELEULEUAA181 - 228187 - 234
36PHEPHELEULEUBB181 - 228187 - 234
46PHEPHELEULEUCC181 - 228187 - 234
17ILEILEARGARGDD237 - 261243 - 267
27ILEILEARGARGAA237 - 261243 - 267
37ILEILEARGARGBB237 - 261243 - 267
47ILEILEARGARGCC237 - 261243 - 267
18ARGARGLEULEUDD267 - 273273 - 279
28ARGARGLEULEUAA267 - 273273 - 279
38ARGARGLEULEUBB267 - 273273 - 279
48ARGARGLEULEUCC267 - 273273 - 279
19GLYGLYGLNGLNDD277 - 290283 - 296
29GLYGLYGLNGLNAA277 - 290283 - 296
39GLYGLYGLNGLNBB277 - 290283 - 296
49GLYGLYGLNGLNCC277 - 290283 - 296

-
Components

#1: Protein
Dihydrodipicolinate synthase / DHDPS


Mass: 31540.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Strain: Serogroup B / Gene: dapA, NMB0929 / Plasmid: pET-151/D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star(DE3) / References: UniProt: Q9JZR4, dihydrodipicolinate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 1.8M ammonium sulfate, 100mM Bis-Tris.HCl, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2008
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.999→115.684 Å / Num. all: 84335 / Num. obs: 84251 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.23 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.349 / Num. unique all: 8359 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.16 Å
Translation2.5 Å41.16 Å

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YXC

1yxc


Resolution: 2→115.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.887 / SU B: 3.03 / SU ML: 0.086 / SU R Cruickshank DPI: 0.152 / SU Rfree: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4201 5 %RANDOM
Rwork0.148 ---
obs0.151 84214 99.87 %-
all-84324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.39 Å2 / Biso mean: 20.562 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.7 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8722 0 264 938 9924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229263
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.98812625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82551209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06524.793363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.642151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031549
X-RAY DIFFRACTIONr_chiral_restr0.090.21473
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026833
X-RAY DIFFRACTIONr_nbd_refined0.2130.24770
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2799
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.229
X-RAY DIFFRACTIONr_mcbond_it1.72626087
X-RAY DIFFRACTIONr_mcangle_it2.25939543
X-RAY DIFFRACTIONr_scbond_it4.4214.53544
X-RAY DIFFRACTIONr_scangle_it6.21263060
Refine LS restraints NCS

Ens-ID: 1 / Number: 1719 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1DMEDIUM POSITIONAL0.21
2AMEDIUM POSITIONAL0.231
3BMEDIUM POSITIONAL0.251
4CMEDIUM POSITIONAL0.21
1DMEDIUM THERMAL1.742
2AMEDIUM THERMAL1.472
3BMEDIUM THERMAL1.522
4CMEDIUM THERMAL1.372
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 276 -
Rwork0.169 5813 -
all-6089 -
obs-5813 99.15 %

+
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