[English] 日本語
Yorodumi
- PDB-2gz3: Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from St... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gz3
TitleStructure of Aspartate Semialdehyde Dehydrogenase (ASADH) from Streptococcus pneumoniae complexed with NADP and aspartate-semialdehyde
ComponentsAspartate beta-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / aspartate pathway
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Aspartate-semialdehyde dehydrogenase, beta-type / Aspartate-semialdehyde dehydrogenase / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-2-AMINO-4-OXOBUTANOIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFaehnle, C.R. / Le Coq, J. / Liu, X. / Viola, R.E.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Examination of key intermediates in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase from a gram-positive infectious bacteria.
Authors: Faehnle, C.R. / Le Coq, J. / Liu, X. / Viola, R.E.
History
DepositionMay 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _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 beta-semialdehyde dehydrogenase
B: Aspartate beta-semialdehyde dehydrogenase
C: Aspartate beta-semialdehyde dehydrogenase
D: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,59612
Polymers160,1544
Non-polymers3,4428
Water14,556808
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aspartate beta-semialdehyde dehydrogenase
B: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7986
Polymers80,0772
Non-polymers1,7214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-31 kcal/mol
Surface area24510 Å2
MethodPISA, PQS
3
C: Aspartate beta-semialdehyde dehydrogenase
hetero molecules

D: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7986
Polymers80,0772
Non-polymers1,7214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area7900 Å2
ΔGint-28 kcal/mol
Surface area24800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.348, 64.439, 96.739
Angle α, β, γ (deg.)89.980, 81.060, 82.000
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Aspartate beta-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: asd / Plasmid: pET 28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8DQ00, UniProt: A0A0H2UPS5*PLUS, aspartate-semialdehyde dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-AS2 / (2R)-2-AMINO-4-OXOBUTANOIC ACID / ASPARTATE SEMIALDEHYDE


Type: D-peptide linking / Mass: 117.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM Citrate pH 6.0 200 mM ammonium acetate 20% PEG 8000 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2006
RadiationMonochromator: Confocal Max-Flux (CMF) multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 3.3 % / Av σ(I) over netI: 6.6 / Number: 192196 / Rmerge(I) obs: 0.113 / Χ2: 0.95 / D res high: 2.3 Å / D res low: 43.58 Å / Num. obs: 57724 / % possible obs: 92.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
4.9543.5897.80.0750.893.34281
3.934.9597.30.0760.863.38243
3.443.9395.90.090.93.24314
3.123.4492.70.1140.893.28163
2.93.12920.1550.933.3194
2.732.991.40.1931.023.399
2.592.7390.70.2271.043.26125
2.482.5990.50.2481.023.3159
2.382.4889.30.27413.3134
2.32.3889.60.2931.013.3130
ReflectionResolution: 2.3→43.58 Å / Num. obs: 95735 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.113 / Χ2: 0.95 / Net I/σ(I): 6.6 / Scaling rejects: 1442
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 3.3 / Num. measured all: 18514 / Num. unique all: 5581 / Χ2: 1.01 / % possible all: 89.6

-
Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2GZ1

2gz1


Resolution: 2.1→30.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.871 / SU B: 13.328 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.325 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3769 5 %RANDOM
Rwork0.211 ---
all0.214 75010 --
obs0.214 75010 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.018 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0.03 Å2
2---0.04 Å2-0.01 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10759 0 224 808 11791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211195
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.98715246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10351411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69725452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.158151849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1991552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21797
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028287
X-RAY DIFFRACTIONr_nbd_refined0.1970.25296
X-RAY DIFFRACTIONr_nbtor_refined0.30.27470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2833
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.2169
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.240
X-RAY DIFFRACTIONr_mcbond_it0.5111.57272
X-RAY DIFFRACTIONr_mcangle_it0.846211425
X-RAY DIFFRACTIONr_scbond_it1.44434482
X-RAY DIFFRACTIONr_scangle_it2.2854.53821
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 257 -
Rwork0.24 5101 -
obs-5358 88.46 %
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)
10.1550.1358-0.06280.4353-0.06910.0261-0.00130.0133-0.02820.03050.00130.0056-0.0141-0.02320-0.03130.00950.00610.0147-0.00320.0048-27.11979.9263-8.2789
20.06110.1072-0.09130.3131-0.07280.20250.00690.006-0.01820.00020.0156-0.0422-0.06690.0025-0.0225-0.01210.0050.0135-0.0096-0.0020.0124-10.82839.3229-19.9663
30.13680.21330.13350.41770.13520.19310.02640.01640.00280.02210.03230.05090.0467-0.0176-0.0587-0.00780.0058-0.0137-0.01020.00980.0011-1.1984-1.2784-62.533
40.12480.11380.12120.49310.07340.1211-0.00520.0220.02330.0040.0267-0.0190.01520.0397-0.0215-0.03440.00340.00840.018-0.0043-0.0048-40.777127.8363-54.8549
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 3582 - 358
22BB2 - 3482 - 348
33CC2 - 3582 - 358
44DD2 - 3582 - 358

+
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://pdbjlvh1.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