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- PDB-3fdu: Crystal structure of a putative enoyl-CoA hydratase/isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 3fdu
TitleCrystal structure of a putative enoyl-CoA hydratase/isomerase from Acinetobacter baumannii
ComponentsPutative enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyLyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta / :
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative enoyl-CoA hydratase/isomerase from Acinetobacter baumannii
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative enoyl-CoA hydratase/isomerase
B: Putative enoyl-CoA hydratase/isomerase
C: Putative enoyl-CoA hydratase/isomerase
D: Putative enoyl-CoA hydratase/isomerase
E: Putative enoyl-CoA hydratase/isomerase
F: Putative enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,44211
Polymers173,9656
Non-polymers4765
Water12,304683
1
A: Putative enoyl-CoA hydratase/isomerase
B: Putative enoyl-CoA hydratase/isomerase
C: Putative enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2676
Polymers86,9833
Non-polymers2843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-70 kcal/mol
Surface area26840 Å2
MethodPISA
2
D: Putative enoyl-CoA hydratase/isomerase
E: Putative enoyl-CoA hydratase/isomerase
F: Putative enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1755
Polymers86,9833
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-67 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.584, 71.731, 132.885
Angle α, β, γ (deg.)90.000, 91.360, 90.000
Int Tables number4
Space group name H-MP1211
Detailstrimer

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Components

#1: Protein
Putative enoyl-CoA hydratase/isomerase


Mass: 28994.230 Da / Num. of mol.: 6 / Mutation: Q11P, Q14N, I59V, K259Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 17978 / Gene: A1S_2548 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3M7S1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5
Details: 100mM Bis-Tris pH 5.0, 23% PEG 3350, 200mM ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→42.563 Å / Num. all: 107766 / Num. obs: 106796 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.5 / Num. measured all: 83491 / Num. unique all: 15347 / Rsym value: 0.302 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 1.083 / WRfactor Rwork: 0.983 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.768 / SU B: 4.581 / SU ML: 0.13 / SU R Cruickshank DPI: 0.204 / SU Rfree: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.283 5416 5.1 %RANDOM
Rwork0.226 ---
obs0.229 106672 99.14 %-
all-107597 --
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 max: 76.48 Å2 / Biso mean: 33.189 Å2 / Biso min: 11.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.6 Å2
2--2.03 Å20 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10370 0 26 683 11079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210574
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.97214371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56351372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.44625.698430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.271151750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4911530
X-RAY DIFFRACTIONr_chiral_restr0.10.21722
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217823
X-RAY DIFFRACTIONr_mcbond_it0.8491.56865
X-RAY DIFFRACTIONr_mcangle_it1.474210922
X-RAY DIFFRACTIONr_scbond_it2.63733709
X-RAY DIFFRACTIONr_scangle_it4.3714.53448
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 375 -
Rwork0.283 7298 -
all-7673 -
obs-7298 97.58 %

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