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- PDB-2y7f: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -

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Basic information

Entry
Database: PDB / ID: 2y7f
TitleCrystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from C. Cloacamonas acidaminovorans in complex with the substrate 3- keto-5-aminohexanoate
Components3-KETO-5-AMINOHEXANOATE CLEAVAGE ENZYME
KeywordsLYASE / ALDOLASE
Function / homology
Function and homology information


(5S)-5-amino-3-oxohexanoate:acetyl-CoA ethylamine transferase / L-lysine fermentation / 3-keto-5-aminohexanoate cleavage activity / 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
(5S)-5-AMINO-3-OXO-HEXANOIC ACID / 3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesCANDIDATUS CLOACAMONAS ACIDAMINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 / 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_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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)125,21813
Polymers124,3514
Non-polymers8679
Water15,709872
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-38.7 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.500, 98.480, 103.180
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(0.0191, 0.0021, -0.9998), (0.0113, -0.9999, -0.0019), (-0.9998, -0.0113, -0.0191)24.8685, -74.526, 24.9173
2given(-0.9899, -0.1401, 0.0207), (-0.1415, 0.982, -0.1251), (-0.0028, -0.1268, -0.9919)-3.4768, 2.5933, 42.497
3given(-0.0407, 0.1234, 0.9915), (0.1115, -0.9856, 0.1272), (0.9929, 0.1157, 0.0263)-17.8306, -77.4062, 26.2376

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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-KMH / (5S)-5-AMINO-3-OXO-HEXANOIC ACID


Mass: 145.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 872 / 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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: NONE
Crystal growpH: 8.5 / Details: 30% PEG4000, 0.2 M MGCL2, 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 20, 2009 / 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: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.75→34.39 Å / Num. obs: 101452 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.93 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 98.7

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Processing

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

2y7d


Resolution: 1.75→33.5 Å / Cor.coef. Fo:Fc: 0.9607 / Cor.coef. Fo:Fc free: 0.9565 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.105 / SU Rfree Blow DPI: 0.094 / SU Rfree Cruickshank DPI: 0.093
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN KAH MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9400. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN KAH MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9400. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=40. NUMBER TREATED BY BAD NON- BONDED CONTACTS=5.
RfactorNum. reflection% reflectionSelection details
Rfree0.1736 5064 5 %RANDOM
Rwork0.1497 ---
obs0.1509 101263 99.71 %-
Displacement parametersBiso mean: 20.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.6107 Å20 Å20 Å2
2---2.9728 Å20 Å2
3---1.3621 Å2
Refine analyzeLuzzati coordinate error obs: 0.158 Å
Refinement stepCycle: LAST / Resolution: 1.75→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8505 0 45 872 9422
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018738HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911858HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4071SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes218HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1281HARMONIC5
X-RAY DIFFRACTIONt_it8702HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.08
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1199SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10983SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2384 362 4.92 %
Rwork0.1975 6996 -
all0.1995 7358 -
obs--99.71 %
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)
10.55760.08820.15010.1177-0.02590.32060.00760.0557-0.0123-0.01510.0197-0.0077-0.0158-0.0171-0.02720.00350.0041-0.0001-0.0170.0025-0.00812.3119-30.7746-1.5758
20.719-0.0094-0.09760.33940.05490.65690.0167-0.0944-0.1252-0.01160.0345-0.02620.02250.0902-0.0512-0.0293-0.0015-0.0096-0.02720.0081-0.004626.5457-43.494222.9779
31.13070.19670.45150.24840.23091.0305-0.0806-0.10810.1763-0.0233-0.02350.065-0.1603-0.03560.1041-0.01360.0117-0.0156-0.0595-0.0165-0.0128-0.8724-27.996147.9994
40.55820.08630.30130.2369-0.00580.7401-0.0351-0.0339-0.0182-0.00130.00620.02930.0369-0.10110.029-0.0173-0.00570.0073-0.0206-0.0037-0.0157-23.2502-46.685925.1668
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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