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- PDB-4rqo: Crystal structure of L-Serine Dehydratase from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4rqo
TitleCrystal structure of L-Serine Dehydratase from Legionella pneumophila
ComponentsL-serine dehydratase
KeywordsLYASE / allosteric substrate binding / type 2 L-serine dehydratase / serine metabolism / iron-sulfur cluster
Function / homologyD-3-phosphoglycerate dehydrogenase; domain 3 / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / IRON/SULFUR CLUSTER / :
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Thunder Bay (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsThoden, J.B. / Holden, H.M. / Grant, G.A.
CitationJournal: Biochemistry / Year: 2014
Title: Structure of l-Serine Dehydratase from Legionella pneumophila: Novel Use of the C-Terminal Cysteine as an Intrinsic Competitive Inhibitor.
Authors: Thoden, J.B. / Holden, H.M. / Grant, G.A.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Data collection
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Oct 16, 2024Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: L-serine dehydratase
B: L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9726
Polymers105,1982
Non-polymers7744
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-97 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.390, 81.390, 267.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsDimer is comprised of chains A+B

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Components

#1: Protein L-serine dehydratase


Mass: 52598.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Thunder Bay (bacteria)
Strain: Philadelphia-1 / Gene: LP6_2208, sdhL / Plasmid: pSV281 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: R9SE63, L-serine ammonia-lyase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Homopipes, 9-13% PEG-3400, 200 mM tetramethylammonium chloride, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 18, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 49999 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 37.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2399 / Rsym value: 0.473 / % possible all: 97.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→29.45 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.889 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.271 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25848 2538 5.1 %RANDOM
Rwork0.19764 ---
obs0.20075 47391 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.631 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.46 Å20 Å2
2---0.46 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6754 0 18 204 6976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196898
X-RAY DIFFRACTIONr_bond_other_d0.0010.026732
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.9969333
X-RAY DIFFRACTIONr_angle_other_deg1.156315532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57525.587281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49151111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0091522
X-RAY DIFFRACTIONr_chiral_restr0.0990.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021451
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.305 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 187 -
Rwork0.257 3388 -
obs--97.97 %

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