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- PDB-2y7d: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -

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Basic information

Entry
Database: PDB / ID: 2y7d
TitleCrystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (orthorombic form)
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
3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesCANDIDATUS CLOACAMONAS ACIDAMINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 1.2May 1, 2024Group: 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 / struct_conn / struct_sheet / 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_sheet.number_strands / _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. THE SHEETS PRESENTED AS "CA" 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 "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-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
C: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
D: 3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,79710
Polymers124,3514
Non-polymers4466
Water17,583976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-187.7 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.870, 100.820, 147.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9562, 0.0184, -0.292), (0.0156, -0.9998, -0.012), (-0.2922, 0.0069, -0.9563)10.0615, 82.5649, 73.8171
2given(-1, 0.0035, 0.0059), (0.0033, 0.9997, -0.0254), (-0.006, -0.0254, -0.9997)0.0799, 1.1511, 76.773
3given(-0.9573, 0.025, 0.2879), (-0.0111, -0.9987, 0.05), (0.2888, 0.0447, 0.9564)-11.7588, 79.9189, -0.128

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Components

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


Mass: 31087.818 Da / Num. of mol.: 4 / 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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / 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: 2.24 Å3/Da / Density % sol: 45.22 % / Description: NONE
Crystal growpH: 7.5
Details: 30% PEG8000, 0.08 M NA ACETATE, 100 MM NA-HEPES PH 7.5 .

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9724
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 27, 2008 / 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: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.59→19.47 Å / Num. obs: 147835 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 6.7 % / Biso Wilson estimate: 20.28 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIAL MODEL FROM SEMET MAD PHASING IN DIFFERENT SPACE GROUP

Resolution: 1.59→19.45 Å / Cor.coef. Fo:Fc: 0.9652 / Cor.coef. Fo:Fc free: 0.9586 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.07
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9408. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=12. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9408. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=12. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 7448 5.04 %RANDOM
Rwork0.1577 ---
obs0.1585 147744 98.51 %-
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.6188 Å20 Å20 Å2
2---3.3384 Å20 Å2
3---0.7196 Å2
Refine analyzeLuzzati coordinate error obs: 0.154 Å
Refinement stepCycle: LAST / Resolution: 1.59→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8367 0 16 976 9359
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018619HARMONIC2
X-RAY DIFFRACTIONt_angle_deg111720HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4037SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes212HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1271HARMONIC5
X-RAY DIFFRACTIONt_it8619HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.17
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1201SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies12HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10757SEMIHARMONIC4
LS refinement shellResolution: 1.59→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2165 496 5.51 %
Rwork0.1982 8505 -
all0.1992 9001 -
obs--98.51 %
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)
10.6162-0.0150.20370.18780.07730.63590.001-0.10730.06480.0213-0.0150.0345-0.0403-0.03070.014-0.0052-0.00180.0094-0.0356-0.0189-0.0314-15.448349.564257.1132
20.74530.073-0.18810.2426-0.04120.6886-0.02780.111-0.0698-0.00180.01530.02720.0499-0.04710.0125-0.01440.00550.0078-0.0494-0.0151-0.0359-20.526332.558824.1071
30.6017-0.03110.12390.2174-0.16790.7108-0.0030.11290.06340.0245-0.009-0.0341-0.10290.02410.0120.01690.00310.0049-0.0430.0168-0.031715.658648.763618.3453
40.5395-0.0665-0.23970.24630.09440.7147-0.0041-0.0975-0.04670.0020.0032-0.02960.00370.04350.0009-0.0124-0.0044-0.0007-0.03290.0084-0.029420.848432.903851.8165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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