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- PDB-2gz1: Structure of Aspartate Semialdehyde Dehydrogenase (ASADH) from St... -

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Basic information

Entry
Database: PDB / ID: 2gz1
TitleStructure of Aspartate Semialdehyde Dehydrogenase (ASADH) from Streptococcus pneumoniae complexed with NADP
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 / isoleucine biosynthetic process / diaminopimelate 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate beta-semialdehyde dehydrogenase
B: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5644
Polymers80,0772
Non-polymers1,4872
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-27 kcal/mol
Surface area24770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.709, 99.165, 64.525
Angle α, β, γ (deg.)90.00, 100.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartate beta-semialdehyde dehydrogenase


Mass: 40038.523 Da / Num. of mol.: 2
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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 48.89 %
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: Nov 1, 2005
RadiationMonochromator: Confocal Max-Flux (CMF) multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 3.64 % / Av σ(I) over netI: 11.4 / Number: 250035 / Rmerge(I) obs: 0.054 / Χ2: 0.94 / D res high: 1.8 Å / D res low: 39.5 Å / Num. obs: 68226 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.8839.599.60.0280.863.67612
3.083.8899.90.0390.853.73379
2.693.0899.90.0550.873.73180
2.442.6999.90.0730.893.69107
2.272.4499.90.0940.933.66118
2.132.2799.90.1431.033.6227
2.032.1399.90.1590.983.697
1.942.031000.1990.973.5839
1.861.941000.2621.083.56103
1.81.861000.31413.5514
ReflectionResolution: 1.8→39.53 Å / Num. all: 68226 / Num. obs: 68226 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.64 % / Rmerge(I) obs: 0.054 / Χ2: 0.94 / Net I/σ(I): 11.4 / Scaling rejects: 1876
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.5 / Num. measured all: 24089 / Num. unique all: 6788 / Χ2: 1 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å39.5 Å
Translation2.5 Å39.5 Å

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Processing

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

2gyy


Resolution: 1.8→39.53 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.601 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 3452 5.1 %RANDOM
Rwork0.16 ---
all0.162 68216 --
obs0.162 68216 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.539 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 96 665 6201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225644
X-RAY DIFFRACTIONr_bond_other_d0.0020.025105
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9797685
X-RAY DIFFRACTIONr_angle_other_deg0.7773.00111894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265712
X-RAY DIFFRACTIONr_chiral_restr0.0720.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026218
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021028
X-RAY DIFFRACTIONr_nbd_refined0.1920.21034
X-RAY DIFFRACTIONr_nbd_other0.2450.26332
X-RAY DIFFRACTIONr_nbtor_other0.080.23334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2539
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.230
X-RAY DIFFRACTIONr_mcbond_it0.4081.53557
X-RAY DIFFRACTIONr_mcangle_it0.80925748
X-RAY DIFFRACTIONr_scbond_it1.55432087
X-RAY DIFFRACTIONr_scangle_it2.5134.51937
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.332 248
Rwork0.296 4739
obs-4987

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