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- PDB-2w02: Co-complex Structure of Achromobactin Synthetase Protein D (AcsD)... -

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Basic information

Entry
Database: PDB / ID: 2w02
TitleCo-complex Structure of Achromobactin Synthetase Protein D (AcsD) with ATP from Pectobacterium Chrysanthemi
ComponentsACSD
KeywordsMETAL TRANSPORT / SSPF / ACSD / ACHROMOBACTIN BIOSYNTHESIS / PECTOBACTERIUM CHRYSANTHEMI
Function / homology
Function and homology information


acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
AcsD, thumb domain, helical bundle / AcsD, palm domain, helix bundle / N-terminal domain of TfIIb - #450 / AscD, thumb domain, four stranded beta-sheet / Double Stranded RNA Binding Domain - #870 / PvsD/AcsD-like, thumb domain, helical bundle / PvsD/AcsD-like, thumb domain, four stranded beta-sheet / PvsD/AcsD-like, palm domain, helix bundle / Aerobactin siderophore biosynthesis, IucA/IucC, N-terminal / Aerobactin siderophore biosynthesis, IucA/IucC-like ...AcsD, thumb domain, helical bundle / AcsD, palm domain, helix bundle / N-terminal domain of TfIIb - #450 / AscD, thumb domain, four stranded beta-sheet / Double Stranded RNA Binding Domain - #870 / PvsD/AcsD-like, thumb domain, helical bundle / PvsD/AcsD-like, thumb domain, four stranded beta-sheet / PvsD/AcsD-like, palm domain, helix bundle / 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 / Endonuclease III; domain 1 / N-terminal domain of TfIIb / Double Stranded RNA Binding Domain / Single Sheet / SH3 type barrels. / DNA polymerase; domain 1 / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / SERINE / AcsD
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchmelz, S. / McMahon, S.A. / Kadi, N. / Song, L. / Oves-Costales, D. / Oke, M. / Liu, H. / Johnson, K.A. / Carter, L. / White, M.F. ...Schmelz, S. / McMahon, S.A. / Kadi, N. / Song, L. / Oves-Costales, D. / Oke, M. / Liu, H. / Johnson, K.A. / Carter, L. / White, M.F. / Challis, G.L. / Naismith, J.H.
CitationJournal: Nat. Chem. Biol. / Year: 2009
Title: AcsD catalyzes enantioselective citrate desymmetrization in siderophore biosynthesis.
Authors: Schmelz, S. / Kadi, N. / McMahon, S.A. / Song, L. / Oves-Costales, D. / Oke, M. / Liu, H. / Johnson, K.A. / Carter, L.G. / Botting, C.H. / White, M.F. / Challis, G.L. / Naismith, J.H.
History
DepositionAug 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACSD
B: ACSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3667
Polymers141,1982
Non-polymers1,1685
Water4,990277
1
A: ACSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1303
Polymers70,5991
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACSD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2364
Polymers70,5991
Non-polymers6373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.874, 94.542, 157.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A7 - 165
2114B7 - 165
2125B166 - 197
2134B198 - 380
1144A381 - 587
2144B381 - 587

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein ACSD


Mass: 70598.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Plasmid: PET151/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q93AT8
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FIVE RESIDUES )IN CHAIN A (MNNRN) AND SEVEN IN CHAIN B (MNNRNHD) RESIDUES ARE DISORDERED. ...THE FIRST FIVE RESIDUES )IN CHAIN A (MNNRN) AND SEVEN IN CHAIN B (MNNRNHD) RESIDUES ARE DISORDERED. RESIDUES 99 (Q) AND 572 - 577 (AEADRQ) IN CHAIN A ARE DISORDERED. IN CHAIN B RESIDUES 98 AND 99 (AQ)ARE DISORDERED. IN BOTH CHAINS THE TERMINAL REDIDUES 587-620 ( GHAVQHGSEVQHDERRHGDVRHEEARHGEVQHG) ARE DISORDERED

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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: 2.13 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M TRIS-HCL PH 7.8, 26% (W/V) PEG8000, 300 MM L-SERINE. 5MM ATP (DISSOLVED IN WATER) WAS PRE-INCUBATED FOR 10 MIN (RT) WITH 6 MG/ML ACSD. PROTEINULLTP PRECIPITATE WAS REMOVED BY ...Details: 0.1 M TRIS-HCL PH 7.8, 26% (W/V) PEG8000, 300 MM L-SERINE. 5MM ATP (DISSOLVED IN WATER) WAS PRE-INCUBATED FOR 10 MIN (RT) WITH 6 MG/ML ACSD. PROTEINULLTP PRECIPITATE WAS REMOVED BY CENTRIFUGATION. 1 UL OF SUPERNATANT AND EQUAL AMOUNT OF PRECIPITANT WAS USED IN HANGING DROP CRYSTALLIZATION (298 K).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2007 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→81.1 Å / Num. obs: 61355 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO STRUCTURE OF ACSD

Resolution: 2.2→81.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.884 / SU B: 20.286 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3096 5 %RANDOM
Rwork0.216 ---
obs0.219 58259 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å20 Å20 Å2
2---3.08 Å20 Å2
3---5.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→81.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9252 0 71 277 9600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0219564
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.95513008
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9523.388487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.318151548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3331587
X-RAY DIFFRACTIONr_chiral_restr0.0860.21381
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027449
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.24823
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2450
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.268
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4951.55901
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82329248
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.27834167
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9394.53760
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1260medium positional0.370.5
12B1260medium positional0.370.5
21A124medium positional0.410.5
22B124medium positional0.410.5
31A1430medium positional0.420.5
32B1430medium positional0.420.5
41A1638medium positional0.380.5
42B1638medium positional0.380.5
21A134loose positional0.685
22B134loose positional0.685
11A1260medium thermal0.522
12B1260medium thermal0.522
21A124medium thermal0.492
22B124medium thermal0.492
31A1430medium thermal0.512
32B1430medium thermal0.512
41A1638medium thermal0.552
42B1638medium thermal0.552
21A134loose thermal1.3910
22B134loose thermal1.3910
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.375 216
Rwork0.315 4261

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