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- PDB-4zbo: Streptomyces bingchenggensis acetoacetate decarboxylase in non-co... -

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Basic information

Entry
Database: PDB / ID: 4zbo
TitleStreptomyces bingchenggensis acetoacetate decarboxylase in non-covalent complex with potassium formate
ComponentsAcetoacetate decarboxylase
KeywordsLYASE / aldolase / dehydratase / acetoacetate decarboxylase
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
Chem-ETE / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Acetoacetate decarboxylase
Similarity search - Component
Biological speciesStreptomyces bingchenggensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 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: 2015
Title: Sbi00515, a Protein of Unknown Function from Streptomyces bingchenggensis, Highlights the Functional Versatility of the Acetoacetate Decarboxylase Scaffold.
Authors: Mydy, L.S. / Hoppe, R.W. / Ochsenwald, J.M. / Berndt, R.T. / Severin, G.B. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 16, 2022Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.6May 17, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.7May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)114,28622
Polymers112,6874
Non-polymers1,60018
Water24,9691386
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22140 Å2
ΔGint-97 kcal/mol
Surface area34060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.900, 124.400, 53.200
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
11C-520-

HOH

DetailsTetramer by Size Exclusion Chromatography

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetoacetate decarboxylase /


Mass: 28171.729 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces bingchenggensis (strain BCW-1) (bacteria)
Strain: BCW-1 / Gene: SBI_00515 / Plasmid: pE-SUMOkan / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star(DE3) / References: UniProt: D7C0E5

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Non-polymers , 5 types, 1404 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1386 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 3.4-3.7 M Potassium formate, 0.1 M bis-tris propane pH 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97896 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97896 Å / Relative weight: 1
ReflectionResolution: 1.4→41.58 Å / Num. obs: 204720 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.5
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIXdev_1702refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→41.58 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 15.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 2960 1.45 %Random selection
Rwork0.1552 ---
obs0.1554 204720 98.41 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7781 0 106 1386 9273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068211
X-RAY DIFFRACTIONf_angle_d1.12211222
X-RAY DIFFRACTIONf_dihedral_angle_d13.9492901
X-RAY DIFFRACTIONf_chiral_restr0.0641212
X-RAY DIFFRACTIONf_plane_restr0.0061479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44580.25662660.226418280X-RAY DIFFRACTION90
1.4458-1.50370.24412910.20519687X-RAY DIFFRACTION97
1.5037-1.57220.20592940.184420013X-RAY DIFFRACTION98
1.5722-1.65510.20222970.173820189X-RAY DIFFRACTION99
1.6551-1.75870.17652970.16920268X-RAY DIFFRACTION100
1.7587-1.89450.17962960.160920389X-RAY DIFFRACTION100
1.8945-2.08520.16633000.151220439X-RAY DIFFRACTION100
2.0852-2.38690.15313030.145520539X-RAY DIFFRACTION100
2.3869-3.00710.17223040.157420682X-RAY DIFFRACTION100
3.0071-41.59930.16973120.142921274X-RAY DIFFRACTION100
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)
13.4067-2.8109-2.92683.31581.82463.17550.0264-0.00220.0410.16340.0388-0.0362-0.00440.0221-0.07450.1844-0.0191-0.02510.19460.00570.173877.683132.654326.5103
20.82830.3334-0.0260.9701-0.71162.9269-0.05040.14990.0177-0.1356-0.0294-0.1298-0.02280.27950.07720.09460.03990.01790.1467-0.00170.158279.127223.5947-4.0141
30.53670.05840.07970.51430.04710.7307-0.00480.0108-0.04230.01390.0084-0.02590.01410.05170.0050.11020.0210.00690.12350.00220.135469.729620.45556.151
41.2861.34490.29891.98870.47510.75070.00790.1164-0.34490.15890.0031-0.15110.19980.05160.00580.20530.0050.00880.2484-0.00610.283282.298520.59742.5476
50.53620.08760.2571.4770.24670.7135-0.00130.04260.0168-0.04960.002-0.0882-0.09090.1273-0.0090.11180.00920.04560.16810.00350.109976.582129.1422.5283
61.7393-0.0961.02820.8856-0.49062.4727-0.01780.11250.0747-0.0623-0.0126-0.10020.01120.2537-0.01170.09990.04630.04490.1613-0.01580.147779.092320.91651.985
72.0336-2.23911.61524.1082-2.10421.34740.00950.0049-0.06950.1795-0.02640.1955-0.1974-0.0732-0.00110.17840.00220.04710.2649-0.04020.298635.620727.529926.4411
80.4731-0.1093-0.03450.39710.00131.24670.02490.2546-0.119-0.146-0.12330.302-0.0881-0.44780.07830.20110.0924-0.06420.3443-0.06910.292933.321438.1565-3.1745
90.76940.286-0.23040.7020.28790.2965-0.02420.0153-0.04420.0148-0.02870.2041-0.0926-0.26680.04470.13050.0702-0.01270.2054-0.02440.207938.338936.91479.4978
100.98410.1571-0.07750.64980.16670.59060.01760.01570.0493-0.0626-0.08260.0631-0.2229-0.14470.0350.18540.0742-0.02410.140.0090.130449.54145.56943.4888
111.3682-0.26340.25633.4021-0.72451.23920.08590.20640.1303-0.1255-0.14620.6796-0.117-0.23430.04150.13750.0363-0.0310.3209-0.0410.30230.113229.53725.0462
120.47540.0869-0.15780.78390.10910.45290.01010.0572-0.0149-0.1005-0.05310.2155-0.1334-0.2240.02930.17220.0909-0.05570.2454-0.01280.219636.800240.36212.0166
131.20520.03751.18825.54393.3933.91840.15060.1383-0.0099-0.2304-0.0653-0.0043-0.1104-0.0894-0.11740.1864-0.00220.01590.16390.01830.139174.267741.95160.5055
140.32670.05550.25940.2861-0.4110.9464-0.0555-0.0420.06870.19480.0322-0.05-0.2006-0.15020.04330.26990.0628-0.00760.111-0.00460.131661.700251.142922.4445
150.5921-0.07810.46030.5003-0.59141.7467-0.0636-0.00340.03350.15810.014-0.0707-0.51260.10850.08630.2707-0.0013-0.01490.1156-0.00630.14867.726549.051124.4451
160.9802-0.02320.0240.4902-0.00260.82140.0090.03290.04390.0431-0.00680.0188-0.2665-0.04550.00880.20950.0264-0.00580.08970.00470.102262.49245.699720.6143
171.7415-1.6064-0.47384.7120.3840.2702-0.0042-0.04310.05220.1787-00.0368-0.1972-0.10210.02240.20510.06340.01640.1287-0.00970.094852.798244.964729.2968
181.3167-1.7031-0.81963.31991.23661.245-0.0917-0.09230.09060.49940.1328-0.4066-0.08330.1768-0.1130.2078-0.0307-0.03410.17190.00570.168282.16340.670221.1294
190.8253-0.1432-0.16180.5114-0.33680.7734-0.0015-0.05490.080.12560.0444-0.0312-0.2543-0.0231-0.04860.23620.017-0.01770.1171-0.0330.114165.202249.484526.1054
200.53021.0761-1.17584.9071-2.48452.60320.09430.03480.0572-0.1438-0.08150.2148-0.064-0.0368-0.05370.1367-0.0016-0.01810.2581-0.05720.270138.239819.37880.0921
211.04290.1935-0.27390.22580.16581.90690.0202-0.2196-0.0590.1892-0.12550.14220.2861-0.15630.10760.2225-0.06150.05620.1311-0.00570.213343.55399.52829.939
220.61450.1362-0.23410.2370.13560.60510.00740.0093-0.05650.0605-0.03150.05880.1295-0.07250.02840.1359-0.01140.01820.10240.00290.164250.824813.445417.9711
231.8071-1.3440.01154.9120.84250.9112-0.0679-0.0803-0.0450.346-0.01260.03820.11030.03690.0590.14880.00090.02030.12240.03010.123259.986815.177827.8842
241.7098-0.52870.55772.9259-0.94081.36880.00180.0234-0.26510.2953-0.10150.34330.0701-0.15210.04950.1702-0.06090.0510.2386-0.0220.235435.568614.068821.6627
250.9547-0.01170.10860.6110.22440.8116-0.0143-0.0717-0.11160.1118-0.02320.10170.1483-0.080.03320.1907-0.03140.04280.15140.03090.199547.67369.949124.7537
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 188 )
5X-RAY DIFFRACTION5chain 'A' and (resid 189 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 263 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 21 )
8X-RAY DIFFRACTION8chain 'B' and (resid 22 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 118 )
10X-RAY DIFFRACTION10chain 'B' and (resid 119 through 170 )
11X-RAY DIFFRACTION11chain 'B' and (resid 171 through 200 )
12X-RAY DIFFRACTION12chain 'B' and (resid 201 through 260 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 21 )
14X-RAY DIFFRACTION14chain 'C' and (resid 22 through 34 )
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 76 )
16X-RAY DIFFRACTION16chain 'C' and (resid 77 through 147 )
17X-RAY DIFFRACTION17chain 'C' and (resid 148 through 170 )
18X-RAY DIFFRACTION18chain 'C' and (resid 171 through 200 )
19X-RAY DIFFRACTION19chain 'C' and (resid 201 through 260 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 21 )
21X-RAY DIFFRACTION21chain 'D' and (resid 22 through 56 )
22X-RAY DIFFRACTION22chain 'D' and (resid 57 through 147 )
23X-RAY DIFFRACTION23chain 'D' and (resid 148 through 170 )
24X-RAY DIFFRACTION24chain 'D' and (resid 171 through 200 )
25X-RAY DIFFRACTION25chain 'D' and (resid 201 through 260 )

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