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- PDB-2gz3: Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from St... -

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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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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