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- PDB-2y7g: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -

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Basic information

Entry
Database: PDB / ID: 2y7g
TitleCrystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the product acetoacetate
Components3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
KeywordsLYASE / ALDOLASE
Function / homology
Function and homology information


3-keto-5-aminohexanoate cleavage enzyme / 3-keto-5-aminohexanoate cleavage activity / L-lysine catabolic process to acetate / metal ion binding
Similarity search - Function
3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETOACETIC ACID / 3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesCANDIDATUS CLOACAMONAS ACIDAMINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBellinzoni, M. / Alzari, P.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: 3-Keto-5-Aminohexanoate Cleavage Enzyme: A Common Fold for an Uncommon Claisen-Type Condensation.
Authors: Bellinzoni, M. / Bastard, K. / Perret, A. / Zaparucha, A. / Perchat, N. / Vergne, C. / Wagner, T. / De Melo-Minardi, R.C. / Artiguenave, F. / Cohen, G.N. / Weissenbach, J. / Salanoubat, M. / Alzari, P.M.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
B: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6519
Polymers62,1762
Non-polymers4767
Water8,971498
1
A: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
B: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
hetero molecules

A: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
B: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,30318
Polymers124,3514
Non-polymers95114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area10760 Å2
ΔGint-193.3 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.100, 102.100, 100.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2131-

HOH

21A-2159-

HOH

31B-2075-

HOH

41B-2091-

HOH

51B-2122-

HOH

61B-2222-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0075, 0.991, 0.134), (0.9925, -0.0237, 0.1196), (0.1216, 0.1321, -0.9837)
Vector: -8.2272, 1.7146, 50.1062)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME


Mass: 31087.818 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDATUS CLOACAMONAS ACIDAMINOVORANS (bacteria)
Plasmid: PCRT7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: B0VHH0

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Non-polymers , 5 types, 505 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.12 Å3/Da / Density % sol: 41.9 % / Description: NONE
Crystal growpH: 7 / Details: 18% PEG3350, 0.220 M MG FORMATE, pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856
DetectorType: ADSC CCD / Detector: CCD / Date: May 22, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.4→45 Å / Num. obs: 104015 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 17.93 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y7D

2y7d


Resolution: 1.4→28 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9462 / SU R Cruickshank DPI: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.058 / SU Rfree Blow DPI: 0.057 / SU Rfree Cruickshank DPI: 0.056
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN AAE MG GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4736. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN AAE MG GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4736. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=20. NUMBER TREATED BY BAD NON- BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 5254 5.06 %RANDOM
Rwork0.1666 ---
obs0.1676 103836 99.18 %-
Displacement parametersBiso mean: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.3491 Å20 Å20 Å2
2--0.3491 Å20 Å2
3----0.6981 Å2
Refine analyzeLuzzati coordinate error obs: 0.157 Å
Refinement stepCycle: LAST / Resolution: 1.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 24 498 4745
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.065900HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2018SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes640HARMONIC5
X-RAY DIFFRACTIONt_it4331HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.68
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion599SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5497SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2128 382 5.09 %
Rwork0.196 7125 -
all0.1968 7507 -
obs--99.18 %
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)
11.5209-0.35520.11750.46630.11480.8367-0.1176-0.00420.1722-0.16460.0310.0309-0.21950.02880.08670.0219-0.0613-0.0186-0.05960.0213-0.0119-0.709338.083120.5791
201.4575-1.65892.5162-0.81630.3215-0.01010.10520.036-0.0056-0.0181-0.09070.0024-0.05210.02810.0222-0.0715-0.040.01280.07430.03073.826438.614510.6147
30.5657-0.02240.14450.5191-0.02920.4666-0.02940.08860.0754-0.0934-0.0421-0.0131-0.0966-0.00020.07150.0075-0.0155-0.0199-0.02010.0044-0.0352-11.845922.648615.8926
40.2861-0.0640.15310.42290.23980.37110.002-0.00370.0513-0.06340.0178-0.1206-0.0130.0396-0.0198-0.0152-0.04210.0097-0.00390.00550.0025.725923.560824.8936
50.3339-0.5843-0.38231.94031.55191.98960.00540.3501-0.0916-0.2803-0.1349-0.0814-0.160.05840.12950.037-0.05640.02880.05560.0273-0.03375.925525.87515.61
60.5962-0.4110.64381.5474-0.33470.5423-0.0711-0.0190.18110.0031-0.0046-0.36450.01220.21080.0757-0.0958-0.00070.02120.02050.02040.02932.46712.828934.5191
71.3048-0.55530.60341.5854-0.05760.1596-0.0903-0.05090.19590.20210.1161-0.26770.04670.1239-0.0258-0.04170.0165-0.01480.0381-0.00410.024830.77820.159140.6234
80.77860.0090.46890.5239-0.15420.68150.0341-0.0285-0.05930.0004-0.03-0.08570.09430.0828-0.0042-0.02350.03240.00970.01270.0225-0.035620.3737-11.543837.0929
91.0258-0.17650.56170.609-0.17760.187-0.0231-0.0976-0.02790.04120.014-0.01370.0340.03910.0092-0.00420.0140.01580.00940.0127-0.02348.6962-3.743434.3917
100.4937-0.05940.01731.1037-0.25280.6393-0.10310.0030.1262-0.01480.0431-0.1564-0.01830.08090.06-0.0479-0.01450.00240.0164-0.00340.013319.507210.243331.8313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A0 - A68 )
2X-RAY DIFFRACTION2(A69 - A80 )
3X-RAY DIFFRACTION3(A81 - A195 )
4X-RAY DIFFRACTION4(A196 - A262 )
5X-RAY DIFFRACTION5(A263 - A275 )
6X-RAY DIFFRACTION6(B0 - B68 )
7X-RAY DIFFRACTION7(B69 - B89 )
8X-RAY DIFFRACTION8(B90 - B154 )
9X-RAY DIFFRACTION9(B155 - B198 )
10X-RAY DIFFRACTION10(B199 - B275 )

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