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- PDB-3uw3: Crystal Structure of an Aspartate-Semialdehyde Dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 3uw3
TitleCrystal Structure of an Aspartate-Semialdehyde Dehydrogenase from Burkholderia Thailandensis
ComponentsAspartate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / dehydrogenase
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, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / 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 ...Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase / Aspartate-semialdehyde dehydrogenase signature. / 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
Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
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 / 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-semialdehyde dehydrogenase
B: Aspartate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7514
Polymers80,6272
Non-polymers1242
Water15,493860
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-42 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.450, 103.100, 106.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate-semialdehyde dehydrogenase


Mass: 40313.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: asd, BTH_II0675 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2T7H5, aspartate-semialdehyde dehydrogenase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Internal tracking number 226078. Wizard 3/4 well F8. 0.1M MMT Buffer/NaOH pH 9.0, 25% w/v PEG1500, 20% Ethylene Glycol for Cryo. ButhA.17885.a.A1 PS01196 CR_24 58.0mg/ml., vapor diffusion, ...Details: Internal tracking number 226078. Wizard 3/4 well F8. 0.1M MMT Buffer/NaOH pH 9.0, 25% w/v PEG1500, 20% Ethylene Glycol for Cryo. ButhA.17885.a.A1 PS01196 CR_24 58.0mg/ml., vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97586 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 28, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97586 Å / Relative weight: 1
ReflectionResolution: 1.55→47.48 Å / Num. all: 123001 / Num. obs: 122928 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 24.061 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.590.4214.7686948996100
1.59-1.630.3465.8676178766100
1.63-1.680.2787.2656918506100
1.68-1.730.2318.6642148337100
1.73-1.790.18810.4616628030100
1.79-1.850.15312.7596197804100
1.85-1.920.12614.9567677512100
1.92-20.10517.6543387261100
2-2.090.08920.3514866976100
2.09-2.190.07623485176658100
2.19-2.310.06625.5455076328100
2.31-2.450.06127.4429856029100
2.45-2.620.05729402155668100
2.62-2.830.05430.9374975287100
2.83-3.10.04733.1343274885100
3.1-3.470.04335.2311264456100
3.47-40.03936.8274123935100
4-4.90.03637.923632335099.9
4.9-6.930.03437.7189042652100
6.930.02936.29621149295.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.48 Å
Translation2.5 Å47.48 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.004data extraction
MD2data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MB4

1mb4


Resolution: 1.55→47.48 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.017 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 6174 5 %RANDOM
Rwork0.151 ---
all0.152 123001 --
obs0.152 122839 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5547 0 8 860 6415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195864
X-RAY DIFFRACTIONr_bond_other_d0.0010.023972
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9777992
X-RAY DIFFRACTIONr_angle_other_deg0.92539774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82124.609230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.209151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7891540
X-RAY DIFFRACTIONr_chiral_restr0.0850.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021133
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 435 -
Rwork0.195 8112 -
all-8547 -
obs-8997 99.91 %
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)
10.2382-0.10660.02890.6111-0.28370.238-0.01720.0025-0.04270.0050.030.04320.03230.0034-0.01280.01640.00830.00570.0202-0.00080.010129.43534.04184.8516
20.3207-0.18910.03660.68660.03680.05740.00220.03390.094-0.0276-0.0092-0.016-0.0128-0.0060.0070.00560.00580.00070.02340.01170.031627.927667.1715-5.0326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 372
2X-RAY DIFFRACTION2B-1 - 373

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