[English] 日本語
Yorodumi
- PDB-3pwk: Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pwk
TitleCrystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus pneumoniae with 2',5'-Adenosine diphosphate and D-2-aminoadipate
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Dehydrogenase / NADP Binding / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Dihydrodipicolinate Reductase; domain 2 / 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
Chem-25A / trans-cyclohexane-1,4-dicarboxylic acid / :
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsPavlovsky, A.G. / Viola, R.E.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family.
Authors: Pavlovsky, A.G. / Liu, X. / Faehnle, C.R. / Potente, N. / Viola, R.E.
History
DepositionDec 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Aspartate-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,97516
Polymers80,0772
Non-polymers2,89814
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-34 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.872, 99.660, 64.436
Angle α, β, γ (deg.)90.00, 100.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Aspartate-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP23-BS72 / Gene: CGSSp23BS72_03388 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21(de3)
References: UniProt: A5MTN0, aspartate-semialdehyde dehydrogenase

-
Non-polymers , 5 types, 783 molecules

#2: Chemical ChemComp-25A / 5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE


Mass: 1005.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N15O19P3
#3: Chemical ChemComp-L14 / trans-cyclohexane-1,4-dicarboxylic acid


Mass: 172.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG 3350, 0.1M MES, 0.1 M ammonium acetate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 4, 2010
RadiationMonochromator: Double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 102882 / % possible obs: 86.6 % / Redundancy: 2.8 % / Rsym value: 0.034 / Net I/σ(I): 22.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 5.1 / Rsym value: 0.18 / % possible all: 43.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2GZ2

2gz2


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.909 / SU ML: 0.033 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15978 5174 5 %RANDOM
Rwork0.13022 ---
obs0.13173 97679 86.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.06 Å2
2--0.58 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5465 0 112 769 6346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225727
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9837789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50425232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68215974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0561527
X-RAY DIFFRACTIONr_chiral_restr0.0880.2910
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214231
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.53599
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81225833
X-RAY DIFFRACTIONr_scbond_it2.85932128
X-RAY DIFFRACTIONr_scangle_it4.3734.51945
X-RAY DIFFRACTIONr_rigid_bond_restr1.2235727
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 184 -
Rwork0.217 3350 -
obs--40.56 %
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)
10.02260.0043-0.03470.0119-0.01360.1893-0.00430.0009-0.00230.0013-0.0035-0.00010.0186-0.01510.00780.0075-0.0008-0.00290.0104-0.00150.00341.577129.306351.6802
20.08640.0119-0.04170.00850.00260.0801-0.0025-0.0009-0.0004-0.0001-0.00090.0005-0.00320.00710.00340.0070.0004-0.0040.01120.00070.002621.248239.754823.0521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 358
2X-RAY DIFFRACTION1A367 - 373
3X-RAY DIFFRACTION1A374 - 1353
4X-RAY DIFFRACTION2B2 - 360
5X-RAY DIFFRACTION2B367 - 373
6X-RAY DIFFRACTION2B375 - 1352

+
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