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- PDB-6eej: Streptomyces bingchenggensis Aldolase-Dehydratase in covalent com... -

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Basic information

Entry
Database: PDB / ID: 6eej
TitleStreptomyces bingchenggensis Aldolase-Dehydratase in covalent complex with dienone product.
ComponentsAcetoacetate decarboxylase
KeywordsLYASE / Secondary metabolism / aldolase / dehydratase
Function / homology
Function and homology information


Acetoacetate decarboxylase-like / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Chem-J6S / : / Acetoacetate decarboxylase
Similarity search - Component
Biological speciesStreptomyces bingchenggensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsMydy, L.S. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1157392 United States
CitationJournal: Biochemistry / Year: 2019
Title: Mechanistic Studies of theStreptomyces bingchenggensisAldolase-Dehydratase: Implications for Substrate and Reaction Specificity in the Acetoacetate Decarboxylase-like Superfamily.
Authors: Mydy, L.S. / Hoppe, R.W. / Hagemann, T.M. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionAug 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetoacetate decarboxylase
B: Acetoacetate decarboxylase
C: Acetoacetate decarboxylase
D: Acetoacetate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,99817
Polymers112,6234
Non-polymers1,37513
Water18,9881054
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19980 Å2
ΔGint-111 kcal/mol
Surface area33460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.050, 123.746, 53.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-656-

HOH

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Components

#1: Protein
Acetoacetate decarboxylase


Mass: 28155.729 Da / Num. of mol.: 4 / Mutation: Y252F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bingchenggensis (strain BCW-1) (bacteria)
Strain: BCW-1 / Gene: SBI_00515 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D7C0E5
#2: Chemical
ChemComp-J6S / (3E,5E)-6-(4-nitrophenyl)-2-oxohexa-3,5-dienoic acid / 4-nitro-cinnamylidenepyruvate, bound form


Mass: 247.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 3.5-4.0 M potassium formate, 2-5% PEG 2K MME, 100 mM Bis-Tris propane, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97985 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97985 Å / Relative weight: 1
ReflectionResolution: 1.892→48.79 Å / Num. obs: 83236 / % possible obs: 99.15 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 17.34
Reflection shellResolution: 1.892→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 7582 / CC1/2: 0.84 / Rpim(I) all: 0.2284 / Rrim(I) all: 0.599 / % possible all: 92.31

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZBO

4zbo


Resolution: 1.892→48.79 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.01
RfactorNum. reflection% reflectionSelection details
Rfree0.1809 2000 2.42 %Random
Rwork0.1615 ---
obs0.1619 82768 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.892→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7898 0 87 1054 9039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028306
X-RAY DIFFRACTIONf_angle_d0.60511383
X-RAY DIFFRACTIONf_dihedral_angle_d10.1094840
X-RAY DIFFRACTIONf_chiral_restr0.0461226
X-RAY DIFFRACTIONf_plane_restr0.0041511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8921-1.93950.22891260.19885107X-RAY DIFFRACTION89
1.9395-1.99190.20351410.17955692X-RAY DIFFRACTION100
1.9919-2.05050.17551430.17035766X-RAY DIFFRACTION100
2.0505-2.11670.21661430.16065761X-RAY DIFFRACTION100
2.1167-2.19240.20461410.1555739X-RAY DIFFRACTION100
2.1924-2.28010.14881440.15065758X-RAY DIFFRACTION100
2.2801-2.38390.16031420.14615784X-RAY DIFFRACTION100
2.3839-2.50960.17371440.15475781X-RAY DIFFRACTION100
2.5096-2.66680.20541440.16165812X-RAY DIFFRACTION100
2.6668-2.87270.18141430.16085804X-RAY DIFFRACTION100
2.8727-3.16170.18011440.16595823X-RAY DIFFRACTION100
3.1617-3.61910.16341460.15735863X-RAY DIFFRACTION100
3.6191-4.55920.14951460.13575920X-RAY DIFFRACTION100
4.5592-48.81110.2071530.19136158X-RAY DIFFRACTION100

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