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- PDB-2iqq: The Crystal Structure of Iron, Sulfur-Dependent L-serine dehydrat... -

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Basic information

Entry
Database: PDB / ID: 2iqq
TitleThe Crystal Structure of Iron, Sulfur-Dependent L-serine dehydratase from Legionella pneumophila subsp. pneumophila
ComponentsIron, Sulfur-Dependent L-serine dehydratase
KeywordsLYASE / alpha-beta / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


L-serine ammonia-lyase / L-serine ammonia-lyase activity / gluconeogenesis / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Iron-sulphur-dependent L-serine dehydratase single chain form / Serine dehydratase-like, alpha subunit / Serine dehydratase beta chain / : / Serine dehydratase alpha chain / Serine dehydratase beta chain / D-3-phosphoglycerate dehydrogenase; domain 3 / Allosteric substrate binding domain superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-serine dehydratase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.66 Å
AuthorsKim, Y. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of Iron, Sulfur-Dependent L-serine dehydratase from Legionella pneumophila subsp. pneumophila
Authors: Kim, Y. / Hatzos, C. / Moy, S. / Joachimiak, A.
History
DepositionOct 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Iron, Sulfur-Dependent L-serine dehydratase
B: Iron, Sulfur-Dependent L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7184
Polymers35,6692
Non-polymers492
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Iron, Sulfur-Dependent L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8592
Polymers17,8351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Iron, Sulfur-Dependent L-serine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8592
Polymers17,8351
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)120.705, 77.151, 56.158
Angle α, β, γ (deg.)90.00, 117.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21B-225-

HOH

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Components

#1: Protein Iron, Sulfur-Dependent L-serine dehydratase / Iron / sulfur-dependent


Mass: 17834.572 Da / Num. of mol.: 2 / Fragment: SDH_beta (residues 4-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Species: Legionella pneumophila / Strain: Philadelphia 1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZXE1, L-serine ammonia-lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.24 Å3/Da / Density % sol: 62.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 50 mM Ammonium sulfate, 50 mM Bis-tris pH 6.5, 30 % Pentaerythritol ethoxylate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.66→38.58 Å / Num. all: 12986 / Num. obs: 12986 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.1
Reflection shellResolution: 2.66→2.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 1.9 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.66→38.58 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 20.518 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1280 9.9 %RANDOM
Rwork0.17435 ---
obs0.17957 11671 98.33 %-
all-11671 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.511 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.02 Å2
2--2.24 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.66→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 2 63 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222348
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9713171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.7765296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30425.596109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.32715420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.113156
X-RAY DIFFRACTIONr_chiral_restr0.1170.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.21154
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2121
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.231
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_it0.7761.51499
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42122340
X-RAY DIFFRACTIONr_scbond_it2.1313930
X-RAY DIFFRACTIONr_scangle_it3.54.5831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 83
Rwork0.342 755
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)
15.5424-0.68550.32525.73540.17483.1230.0395-0.3563-0.08020.76380.05460.63070.31120.1015-0.0941-0.21920.04520.099-0.19550.0777-0.19841.47929.915331.6703
24.17450.6030.81965.78760.5224.22420.06690.1570.2888-0.93250.0622-0.22340.00830.2515-0.1291-0.1388-0.06150.0199-0.2185-0.0007-0.283313.908939.96178.1611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA14 - 15817 - 161
2X-RAY DIFFRACTION2BB14 - 15817 - 161

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