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- PDB-2x0o: Apo structure of the Alcaligin biosynthesis protein C (AlcC) from... -

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Basic information

Entry
Database: PDB / ID: 2x0o
TitleApo structure of the Alcaligin biosynthesis protein C (AlcC) from Bordetella bronchiseptica
ComponentsALCALIGIN BIOSYNTHESIS PROTEIN
KeywordsBIOSYNTHETIC PROTEIN / ALCALIGIN BIOSYNTHESIS / ADENYLATION / SIDEROPHORES / IRON ACQUISITION
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process
Similarity search - Function
Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Transferase(Phosphotransferase); domain 1 - #40 / TATA-Binding Protein - #280 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3370 / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like / IucA / IucC family / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter / TATA-Binding Protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Transferase(Phosphotransferase); domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesBORDETELLA BRONCHISEPTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJohnson, K.A. / Schmelz, S. / Kadi, N. / Mcmahon, S.A. / Oke, M. / Liu, H. / Carter, L.G. / White, M.F. / Challis, G.L. / 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
DepositionDec 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5286
Polymers70,0481
Non-polymers4805
Water3,207178
1
A: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules

A: ALCALIGIN BIOSYNTHESIS PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,05712
Polymers140,0962
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6040 Å2
ΔGint-161.5 kcal/mol
Surface area41770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.667, 128.910, 48.261
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALCALIGIN BIOSYNTHESIS PROTEIN / ALCC


Mass: 70047.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Plasmid: PET-151/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94255
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6
Details: 1.4M MG-SULFATE, 0.1M NA-CACODYLATE, PH6.0, 0.1M LI-SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.000005
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000005 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 23068 / % possible obs: 97.9 % / Observed criterion σ(I): 3.3 / Redundancy: 4.1 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FFE

3ffe


Resolution: 2.4→42.901 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1151 5 %
Rwork0.1817 --
obs0.1844 23068 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.938 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.9078 Å2-0 Å20 Å2
2---9.5951 Å2-0 Å2
3---3.6873 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4631 0 25 178 4834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034785
X-RAY DIFFRACTIONf_angle_d0.7256519
X-RAY DIFFRACTIONf_dihedral_angle_d17.091713
X-RAY DIFFRACTIONf_chiral_restr0.049696
X-RAY DIFFRACTIONf_plane_restr0.003845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4005-2.50970.28421620.21942627X-RAY DIFFRACTION97
2.5097-2.6420.29511330.21842753X-RAY DIFFRACTION99
2.642-2.80750.27641390.20562728X-RAY DIFFRACTION99
2.8075-3.02430.28551160.2082786X-RAY DIFFRACTION99
3.0243-3.32850.23941710.192686X-RAY DIFFRACTION99
3.3285-3.80990.25471380.17022748X-RAY DIFFRACTION98
3.8099-4.7990.1861370.14012772X-RAY DIFFRACTION97
4.799-42.90810.18671550.17212817X-RAY DIFFRACTION95
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)
10.4599-0.1287-0.06010.5260.42660.3274-0.0146-0.0295-0.0956-0.0178-0.02860.23020.0996-0.09450.02630.0672-0.0423-0.01110.07270.01280.108519.6274-7.14084.3116
20.6875-0.4688-0.00340.8141-0.32410.2019-0.0117-0.2024-0.03140.04820.0495-0.03-0.0394-0.0147-0.01930.0735-0.003-0.01890.08870.0090.064626.84413.940316.2712
31.33550.0880.15830.6460.11420.6317-0.0521-0.05170.0564-0.03320.0216-0.02180.0091-0.02130.01990.0455-0.0059-0.00340.0453-0.01390.013246.280718.593921.7203
41.0775-0.5650.15410.4944-0.0050.0398-0.03310.2260.19490.0051-0.055-0.1634-0.0783-0.00340.05430.0420.00230.00650.06370.00460.079138.26826.353310.8614
50.5441-0.320.1190.9731-0.37070.54880.0003-0.00490.0652-0.1045-0.02650.01990.08470.01870.01730.070.0217-0.01450.0830.00930.041817.78121.22764.7397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 7:116)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 117:173)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 174:320)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 321:385)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 386:601)

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