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- PDB-3q1l: Crystals Structure of Aspartate beta-Semialdehyde Dehydrogenase f... -

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Basic information

Entry
Database: PDB / ID: 3q1l
TitleCrystals Structure of Aspartate beta-Semialdehyde Dehydrogenase from Streptococcus pneumoniae with cysteamine bound covalently to Cys 128
ComponentsAspartate beta-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / NADP / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
2-AMINO-ETHANETHIOL / Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 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 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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

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)160,4638
Polymers160,1544
Non-polymers3094
Water6,143341
1
A: Aspartate beta-semialdehyde dehydrogenase
B: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2314
Polymers80,0772
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-26 kcal/mol
Surface area25570 Å2
MethodPISA
2
C: Aspartate beta-semialdehyde dehydrogenase
D: Aspartate beta-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2314
Polymers80,0772
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-27 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.611, 78.840, 244.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Strain: ATCC BAA-255 / R6 / Gene: asd, CGSSpBS455_08742, spr0918 / Plasmid: pET 28a / Production host: Escherichia coli (E. coli) / Strain (production host): bl21 (de3)
References: UniProt: Q8DQ00, aspartate-semialdehyde dehydrogenase
#2: Chemical
ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7NS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 13% PEG 3350, 0.1 M MES buffer, 0.05 M Ca-acetate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 28, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→23 Å / Num. obs: 55295 / % possible obs: 83 % / Redundancy: 2.9 % / Rsym value: 0.057 / Net I/σ(I): 13.6
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.303 / % possible all: 44.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→23 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.919 / SU B: 16.611 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24209 2711 5 %RANDOM
Rwork0.19361 ---
obs0.19606 51590 85.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2--0.05 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10905 0 16 341 11262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211137
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1371.96515126
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84151429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59425.043462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.217151893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2261552
X-RAY DIFFRACTIONr_chiral_restr0.0780.21768
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218290
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_it0.3831.57126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.739211525
X-RAY DIFFRACTIONr_scbond_it1.18734011
X-RAY DIFFRACTIONr_scangle_it1.9694.53600
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 143 -
Rwork0.245 2593 -
obs--58.94 %
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)
10.3112-0.2177-0.25821.01140.87621.60840.00940.0504-0.0340.0376-0.12560.03990.0289-0.1170.11620.2398-0.038-0.0090.06750.00040.0583.73815.81812.839
20.9397-0.6344-0.68220.84390.87431.9481-0.066-0.20250.13010.2772-0.0501-0.02520.0181-0.06250.11610.3968-0.0829-0.00440.1457-0.05210.0518-2.13132.27245.022
31.0332-0.56421.03710.5545-0.64931.85190.07760.04210.093-0.0373-0.1022-0.00270.05070.08380.02460.2559-0.02260.00910.05930.0070.068528.245-14.90516.4
41.8395-0.27810.88850.458-0.19341.5961-0.0622-0.60150.1170.167-0.0345-0.0075-0.129-0.06880.09680.3319-0.0707-0.02790.2898-0.03560.015641.476-18.08850.024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 358
2X-RAY DIFFRACTION1A367
3X-RAY DIFFRACTION1A368 - 596
4X-RAY DIFFRACTION2B2 - 357
5X-RAY DIFFRACTION2B367
6X-RAY DIFFRACTION2B368 - 595
7X-RAY DIFFRACTION3C2 - 361
8X-RAY DIFFRACTION3C367
9X-RAY DIFFRACTION3C368 - 600
10X-RAY DIFFRACTION4D2 - 357
11X-RAY DIFFRACTION4D367
12X-RAY DIFFRACTION4D368 - 599

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