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- PDB-2iaf: Crystal structure of a fragment (residues 11 to 161) of L-serine ... -

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Entry
Database: PDB / ID: 2iaf
TitleCrystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila
ComponentsHypothetical protein sdhL
Keywordsstructural genomics / unknown function / MCSG / PSI2 / MAD / L-serine dehydratase / Protein Structure Initiative / Midwest Center for Structural Genomics
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsNocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a fragment (residues 11 to 161) of L-serine dehydratase from Legionella pneumophila
Authors: Nocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A.
History
DepositionSep 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein sdhL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7912
Polymers16,7661
Non-polymers241
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.319, 76.835, 108.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-149-

MG

21A-197-

HOH

31A-204-

HOH

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Components

#1: Protein Hypothetical protein sdhL / L-serine dehydratase


Mass: 16766.432 Da / Num. of mol.: 1 / Fragment: Residues 11-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: sdhL / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5WYB1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 Ammonium sulphate, 0.1M BisTris pH 6.5, 25% Peg 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793, 0.97943
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2006
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.979431
ReflectionResolution: 2.05→40 Å / Num. all: 15069 / Num. obs: 14934 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.478 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.05→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.589 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22418 756 5.1 %RANDOM
Rwork0.19455 ---
obs0.19602 14168 99.04 %-
all-14930 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 1 87 1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.9731510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6535140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30625.57752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.645153
X-RAY DIFFRACTIONr_chiral_restr0.1560.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.2486
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2752
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3891.5717
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99621112
X-RAY DIFFRACTIONr_scbond_it2.8863444
X-RAY DIFFRACTIONr_scangle_it4.3924.5398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 64 -
Rwork0.259 1032 -
obs--99.28 %
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)
123.69683.174215.215333.11653.199824.6327-1.84730.1251.2375-0.88071.1192-1.5835-1.9158-0.08830.7280.1117-0.12780.00090.0143-0.13810.222414.261736.606314.8667
22.2888-1.65163.93149.6139-0.78057.2549-0.3254-0.21920.04010.32850.5028-1.5963-0.23750.3245-0.1774-0.0462-0.0427-0.01390.1072-0.16490.327217.635826.513319.8349
31.81866.5130.129530.8515-7.63768.73010.0864-0.5148-0.43560.9795-0.0733-2.00710.04230.4865-0.0131-0.05020.0975-0.2170.1185-0.03440.363519.283816.941327.3203
45.4534-0.52461.3866.8790.89586.3464-0.1150.2451-0.3642-0.07950.2014-1.44020.18990.0522-0.0864-0.0103-0.00120.0250.0075-0.06710.430716.590611.552718.7334
51.938-3.32710.76497.0353-2.34862.7912-0.26640.0505-0.0292-0.25360.2612-0.4946-0.1767-0.18250.00530.1026-0.04360.02130.1333-0.11720.06654.793128.934413.949
618.0272-9.4991-0.36349.6995-1.64820.72830.640.82850.2946-1.0503-0.3601-0.7037-0.1869-0.0082-0.280.1717-0.02780.17560.0289-0.0730.238113.57629.04378.3587
78.74798.12267.629424.18575.72266.7653-0.3085-0.5269-0.0802-0.50680.414-2.12790.06450.1195-0.1055-0.1653-0.06160.179-0.0146-0.18610.541622.91925.947114.8244
822.021318.030714.956116.40128.463418.8911-1.0288-0.2244-0.4533-1.20350.5661-2.3681-1.4764-0.32220.4627-0.0808-0.07280.3568-0.0267-0.07890.377222.621428.78186.5703
90.60390.67632.02244.26590.97917.24350.10510.1857-0.0914-0.39470.1159-0.84950.12940.3026-0.2210.0194-0.01270.28190.0099-0.06060.31419.705118.47956.8425
106.0222-4.3572.42243.6161-1.49933.13930.09420.0020.4029-0.5677-0.0601-0.67660.1591-0.0168-0.03410.1005-0.0730.19060.0358-0.10560.218113.193916.03579.4236
115.33351.80093.65287.27764.06097.3216-0.1894-0.27410.3523-0.09390.1136-0.1509-0.1004-0.49240.07580.08790.0093-0.01440.149-0.0939-0.03091.154630.18317.1556
121.78650.9536-0.48090.8487-1.14812.4683-0.1305-0.3668-0.1760.30530.0983-0.61850.16510.03280.03220.0625-0.00040.03550.1166-0.0740.13869.075314.366519.744
131.28440.31580.239710.1506-2.11710.879-0.1915-0.43190.06630.28110.1178-0.5323-0.0273-0.21430.07370.08760.0202-0.04170.171-0.12090.06529.233122.892624.489
1417.34264.3410.489918.0009-16.027415.43410.35290.36950.61860.2645-0.3561-1.2567-1.04210.24770.00320.20940.0841-0.04410.0393-0.23360.221913.600937.395722.744
157.9318-0.9332-3.023620.69334.327619.3284-0.8761-0.78390.3410.880.6991-0.53580.1709-0.08610.17690.12480.1252-0.17730.1413-0.1830.01098.291531.364931.1649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 97 - 12
2X-RAY DIFFRACTION2AA10 - 1813 - 21
3X-RAY DIFFRACTION3AA19 - 2622 - 29
4X-RAY DIFFRACTION4AA27 - 3330 - 36
5X-RAY DIFFRACTION5AA34 - 4437 - 47
6X-RAY DIFFRACTION6AA45 - 5748 - 60
7X-RAY DIFFRACTION7AA58 - 6361 - 66
8X-RAY DIFFRACTION8AA64 - 7467 - 77
9X-RAY DIFFRACTION9AA75 - 8978 - 92
10X-RAY DIFFRACTION10AA90 - 10093 - 103
11X-RAY DIFFRACTION11AA101 - 114104 - 117
12X-RAY DIFFRACTION12AA115 - 126118 - 129
13X-RAY DIFFRACTION13AA127 - 133130 - 136
14X-RAY DIFFRACTION14AA134 - 140137 - 143
15X-RAY DIFFRACTION15AA141 - 148144 - 151

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