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- PDB-2x4l: Crystal structure of DesE, a ferric-siderophore receptor protein ... -

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Basic information

Entry
Database: PDB / ID: 2x4l
TitleCrystal structure of DesE, a ferric-siderophore receptor protein from Streptomyces coelicolor
ComponentsFERRIC-SIDEROPHORE RECEPTOR PROTEIN
KeywordsTRANSPORT
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRIC-SIDEROPHORE RECEPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)34,5761
Polymers34,5761
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.840, 57.540, 102.970
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 FERRIC-SIDEROPHORE RECEPTOR PROTEIN


Mass: 34575.973 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: A3(2) / Plasmid: PET151 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9L074
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.23 Å3/Da / Density % sol: 44.77 % / Description: NONE
Crystal growpH: 6
Details: FROM 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL. CRYSTAL WAS CRYOPROTECTED BY 3.4M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.25M NACL. PHASES WERE DETERMINED BY SOAKING CRYSTAL IN ...Details: FROM 2.63M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.24M NACL. CRYSTAL WAS CRYOPROTECTED BY 3.4M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.25M NACL. PHASES WERE DETERMINED BY SOAKING CRYSTAL IN 2.8M SODIUM MALONATE, 0.1M BISTRIS PH 6.0, 0.5M NABR FOR 1 MINUTE PRIOR TO CRYOPROTECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 50077 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.17
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→29.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.602 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20941 2544 5.1 %RANDOM
Rwork0.17909 ---
obs0.18061 47533 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.161 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 0 212 2479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.973148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69525.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51215390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.954158
X-RAY DIFFRACTIONr_chiral_restr0.1440.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211723
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_it1.2811.51488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.98622396
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4553826
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5684.5752
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 196 -
Rwork0.22 3467 -
obs--100 %
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)
11.5121-0.905-0.80082.91420.3613-0.0752-0.2130.0223-0.29120.16160.02120.18290.1809-0.07910.19180.1277-0.0920.08310.1264-0.04960.09592.79719.32632.24
20.872-0.0712-0.69940.17370.24091.4245-0.0721-0.0069-0.00710.04730.01390.04270.009-0.05240.05820.059-0.0023-0.00010.03680.00520.051512.44232.77829.301
32.5444-1.172-3.49071.87760.12613.793-0.35260.7637-0.2382-0.11230.07270.05420.652-0.87160.27990.1396-0.17160.05040.2261-0.07770.0713.71822.45420.032
44.4887-0.7047-2.24220.48961.11494.051-0.0690.0845-0.1281-0.1149-0.13870.13810.0162-0.42520.20770.04560.0061-0.03340.1232-0.04390.06378.11625.1674.357
50.6982-0.53150.39460.9602-0.25841.2483-0.02240.08820.07410.0812-0.0998-0.14480.01320.12990.12220.0252-0.0239-0.0080.04480.01450.072331.65926.94812.349
61.381-0.07460.00850.60220.24431.50060.0290.14430.1171-0.0527-0.0557-0.0626-0.18270.01510.02670.061-0.0172-0.00240.0250.01510.051425.80434.8117.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 68
2X-RAY DIFFRACTION2A69 - 177
3X-RAY DIFFRACTION3A178 - 193
4X-RAY DIFFRACTION4A194 - 219
5X-RAY DIFFRACTION5A220 - 294
6X-RAY DIFFRACTION6A295 - 349

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