[English] 日本語
Yorodumi
- PDB-2rfg: Crystal structure of dihydrodipicolinate synthase from Hahella ch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rfg
TitleCrystal structure of dihydrodipicolinate synthase from Hahella chejuensis at 1.5A resolution
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / BETA 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 / cytoplasm
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
ETHANOL / 4-hydroxy-tetrahydrodipicolinate synthase
Similarity search - Component
Biological speciesHahella chejuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKang, B.S. / Kim, M.H. / Kim, G.H. / Kim, K.J.
CitationJournal: to be published
Title: Crystal structure of dihydrodipicolinate synthase from Hahella chejuensis at 1.5A resolution
Authors: Kang, B.S. / Kim, M.H. / Kim, G.H. / Kim, K.J.
History
DepositionSep 29, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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)129,4146
Polymers129,3444
Non-polymers702
Water28,1931565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.061, 120.644, 161.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Dihydrodipicolinate synthase /


Mass: 32335.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hahella chejuensis (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q2S9K4, dihydrodipicolinate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1565 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% ethanol, 0.2M magnesium chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 255980 / Redundancy: 5.9 % / Rsym value: 0.063 / Net I/σ(I): 30.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.35

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DHP

1dhp


Resolution: 1.5→19.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.118 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17792 10481 5 %RANDOM
Rwork0.15907 ---
obs0.16001 198273 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8835 0 4 1565 10404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229243
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.96712621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99451229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47224.104402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.824151536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0191564
X-RAY DIFFRACTIONr_chiral_restr0.0840.21449
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027077
X-RAY DIFFRACTIONr_nbd_refined0.2060.24810
X-RAY DIFFRACTIONr_nbtor_refined0.3070.26541
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.21224
X-RAY DIFFRACTIONr_metal_ion_refined0.030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.250
X-RAY DIFFRACTIONr_mcbond_it0.5921.56056
X-RAY DIFFRACTIONr_mcangle_it0.929542
X-RAY DIFFRACTIONr_scbond_it1.68333510
X-RAY DIFFRACTIONr_scangle_it2.6384.53044
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 765 -
Rwork0.205 14150 -
obs--97.75 %
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)
10.40530.0597-0.12830.4519-0.04080.15960.02580.0127-0.01760.0017-0.01310.0199-0.0325-0.0067-0.0127-0.0499-0.0021-0.0057-0.0256-0.0128-0.0391-27.38-20.6134.073
20.60550.17760.21240.67090.16460.3923-0.0039-0.02980.00190.0847-0.00360.0598-0.0009-0.05940.0075-0.009-0.00340.0123-0.04180.0106-0.0418-45.084-16.7436.289
30.47950.16210.16330.51910.13530.5275-0.0152-0.01070.0028-0.03030.0299-0.0128-0.03740.0551-0.0147-0.0084-0.0024-0.0024-0.0521-0.0149-0.0491-22.8438.52843.602
40.34570.08040.06831.1490.09560.53630.0370.01870.02380.001-0.0028-0.0246-0.14320.0464-0.03430.0104-0.01980.0344-0.0349-0.0106-0.0405-15.39410.6067.556
50.1091-0.0102-0.02060.15290.08790.17970.01240.0009-0.0010.00310.0101-0.0127-0.03930.003-0.02250.0044-0.0014-0.0024-0.0153-0.0023-0.0031-28.164-4.85922.98
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 288
2X-RAY DIFFRACTION2B2 - 297
3X-RAY DIFFRACTION3C1 - 289
4X-RAY DIFFRACTION4D1 - 289
5X-RAY DIFFRACTION5A502 - 912
6X-RAY DIFFRACTION5C298 - 701
7X-RAY DIFFRACTION5B298 - 687
8X-RAY DIFFRACTION5D300 - 656

+
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