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- PDB-3c8w: Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.... -

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Basic information

Entry
Database: PDB / ID: 3c8w
TitleCrystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution
ComponentsAcetoacetate decarboxylase ADC
KeywordsLYASE / YP_094708.1 / acetoacetate decarboxylase (ADC) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


acetoacetate decarboxylase / acetoacetate decarboxylase activity
Similarity search - Function
Acetoacetate decarboxylase-like / Acetoacetate decarboxylase-like / Acetoacetate decarboxylase / Acetoacetate decarboxylase domain superfamily / Acetoacetate decarboxylase (ADC) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Acetoacetate decarboxylase ADC
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Acetoacetate decarboxylase ADC
B: Acetoacetate decarboxylase ADC
C: Acetoacetate decarboxylase ADC
D: Acetoacetate decarboxylase ADC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9348
Polymers115,1654
Non-polymers7684
Water12,809711
1
A: Acetoacetate decarboxylase ADC
B: Acetoacetate decarboxylase ADC
C: Acetoacetate decarboxylase ADC
D: Acetoacetate decarboxylase ADC
hetero molecules

A: Acetoacetate decarboxylase ADC
B: Acetoacetate decarboxylase ADC
C: Acetoacetate decarboxylase ADC
D: Acetoacetate decarboxylase ADC
hetero molecules

A: Acetoacetate decarboxylase ADC
B: Acetoacetate decarboxylase ADC
C: Acetoacetate decarboxylase ADC
D: Acetoacetate decarboxylase ADC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)347,80124
Polymers345,49512
Non-polymers2,30512
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area59170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.100, 104.100, 189.640
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: ALA / Refine code: 2 / Auth seq-ID: 6 - 254 / Label seq-ID: 7 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Acetoacetate decarboxylase ADC


Mass: 28791.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Species: Legionella pneumophila / Strain: Philadelphia 1 / DSM 7513
Description: SYNTHETIC GENE: The gene product was based on YP_094708.1 (acetoacetate decarboxylase (ADC) / lpg0672) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Gene: YP_094708.1, lpg0672 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5ZXQ9, acetoacetate decarboxylase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 0.5M (NH4)2SO4, 1.0M Li2SO4, 0.1M Citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 10, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979011
ReflectionResolution: 1.6→29.683 Å / Num. obs: 142031 / % possible obs: 80.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.188 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.27
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.660.6221.43760020973166.3
1.66-1.720.581.84860719568171.3
1.72-1.80.512.38026425102180.5
1.8-1.90.39838799626597183.2
1.9-2.020.2734.58405025376183.6
2.02-2.170.1936.38145124555184
2.17-2.390.1329.18516925700184.2
2.39-2.730.09138420225395184.6
2.73-3.440.04623.48607125973184.9
3.44-29.6830.02343.18570326005185

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→29.683 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.793 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.096
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE ELECTRON DENSITY REVEALS THAT LYSINE 125 HAS FORMED A SCHIFF BASE. IT WAS MODELED AS THE ENZYME-ACETOACETATE SCHIFF BASE INTERMEDIATE, WHICH IS CONSISTENT WITH THE OBSERVED ELECTRON DENSITY AND THE PUTATIVE ENZYMATIC MECHANISM. 5. CITRATE ANIONS FROM CRYSTALLIZATION ARE MODELED IN THIS STRUCTURE. 6. POOR ELECTRON DENSITY AROUND RESIDUE 11, 12 AND 13 IN EACH SUBUNIT RESULTS IN RAMACHANDRAN OUTLIERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 7169 5 %RANDOM
Rwork0.193 ---
obs0.195 142031 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7780 0 52 711 8543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228142
X-RAY DIFFRACTIONr_bond_other_d0.0010.025459
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.99311130
X-RAY DIFFRACTIONr_angle_other_deg1.044313403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57551016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.73824.076314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.352151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.141529
X-RAY DIFFRACTIONr_chiral_restr0.0970.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021584
X-RAY DIFFRACTIONr_mcbond_it1.70535064
X-RAY DIFFRACTIONr_mcbond_other0.67832006
X-RAY DIFFRACTIONr_mcangle_it2.58158255
X-RAY DIFFRACTIONr_scbond_it4.33783078
X-RAY DIFFRACTIONr_scangle_it6.281112875
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1423TIGHT POSITIONAL0.140.05
2B1423TIGHT POSITIONAL0.120.05
3C1423TIGHT POSITIONAL0.140.05
4D1423TIGHT POSITIONAL0.130.05
1A1747MEDIUM POSITIONAL0.210.5
2B1747MEDIUM POSITIONAL0.210.5
3C1747MEDIUM POSITIONAL0.380.5
4D1747MEDIUM POSITIONAL0.230.5
1A1423TIGHT THERMAL0.830.5
2B1423TIGHT THERMAL0.880.5
3C1423TIGHT THERMAL0.860.5
4D1423TIGHT THERMAL0.860.5
1A1747MEDIUM THERMAL0.972
2B1747MEDIUM THERMAL1.032
3C1747MEDIUM THERMAL1.062
4D1747MEDIUM THERMAL0.992
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 437 -
Rwork0.318 8848 -
all-9285 -
obs--82.89 %
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)
10.34920.0683-0.12020.1348-0.15390.60860.0120.0066-0.0674-0.0103-0.0053-0.06270.07260.0231-0.0067-0.02920.02090-0.0304-0.01120.007527.07336.44582.036
20.40660.1446-0.08340.3742-0.02260.12270.004-0.0536-0.02530.04570.0087-0.03450.0150.0323-0.0127-0.01140.0091-0.0222-0.01520.0164-0.026413.08338.735121.155
30.44-0.18960.01620.4061-0.02640.19670.00250.04880.0208-0.05130.0053-0.0184-0.01050.0277-0.0077-0.01940.00110.0216-0.0081-0.0076-0.032923.98460.01863.726
40.1019-0.03830.01510.28310.23630.3530.0072-0.00090.028-0.00850.0011-0.0809-0.01760.0286-0.0083-0.0359-0.0009-0.0078-0.0118-0.0060.008734.18870.123104.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2546 - 255
2X-RAY DIFFRACTION2BB6 - 2547 - 255
3X-RAY DIFFRACTION3CC6 - 2547 - 255
4X-RAY DIFFRACTION4DD5 - 2546 - 255

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