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- PDB-4fha: Structure of Dihydrodipicolinate Synthase from Streptococcus pneu... -

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Basic information

Entry
Database: PDB / ID: 4fha
TitleStructure of Dihydrodipicolinate Synthase from Streptococcus pneumoniae,bound to pyruvate and lysine
ComponentsDihydrodipicolinate synthase
KeywordsLYASE / 8-fold alpha-/beta-barrel / L-aspartate-4-semialdehyde hydro-lyase
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / LYSINE / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPerugini, M.A. / Dogovski, C. / Parker, M.W. / Gorman, M.A.
CitationJournal: To be Published
Title: Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae
Authors: Perugini, M.A. / Dogovski, C. / Parker, M.W. / Gorman, M.A. / Dobson, R.C.J. / Jameson, G.B. / Ketaren, N.E. / Praszkier, J. / Bailey, M.F. / Bryant, G. / Yang, J. / Griffin, M.D.W. / Pearce, F.G. / Mitsakos, V.
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3726
Polymers68,0312
Non-polymers3404
Water5,909328
1
A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules

A: Dihydrodipicolinate synthase
B: Dihydrodipicolinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,74412
Polymers136,0634
Non-polymers6818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area11270 Å2
ΔGint-97 kcal/mol
Surface area41590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.381, 106.368, 106.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Dihydrodipicolinate synthase /


Mass: 34015.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: SP3-BS71 / Gene: CGSSp3BS71_00085 / Plasmid: pET101/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5LD17, dihydrodipicolinate synthase
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M sodium fluoride, 0.1 M bis-tris propane, 20% (w/v) PEG 3350, 5% (w/v) 1,4-dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95371 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 5, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.438
11-H, L, K20.562
ReflectionResolution: 1.88→75.18 Å / Num. all: 55338 / Num. obs: 55338 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rsym value: 0.076 / Net I/σ(I): 27.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.88-1.988.60.342.25980169870.3486.7
1.98-2.114.40.2343.211104077050.23499.9
2.1-2.2514.90.1684.410792972660.168100
2.25-2.4314.80.1295.710053867790.129100
2.43-2.6614.80.0987.59250762610.098100
2.66-2.9714.60.0789.48246756660.078100
2.97-3.4314.30.063117208550510.063100
3.43-4.214.10.05512.86069242970.055100
4.2-5.94140.05113.34725833830.051100
5.94-47.55712.50.04215.12432519430.04298.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H5D

3h5d
PDB Unreleased entry


Resolution: 1.88→39.91 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.1818 / WRfactor Rwork: 0.1589 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8367 / SU B: 3.351 / SU ML: 0.094 / SU R Cruickshank DPI: 0.0257 / SU Rfree: 0.0232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: AMPLITUDE BASED TWIN REFINEMENT USED
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 2754 5 %RANDOM
Rwork0.1587 ---
obs0.1599 55281 97.71 %-
all-56520 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.31 Å2 / Biso mean: 20.8595 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1-10.92 Å20 Å20 Å2
2---9.92 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 22 328 5078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024871
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9766622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6525208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79715782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9051516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213706
LS refinement shellResolution: 1.88→1.927 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 145 -
Rwork0.193 2970 -
all-3115 -
obs--75.21 %

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