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- PDB-2y7e: Crystal structure of the 3-keto-5-aminohexanoate cleavage enzyme ... -

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Basic information

Entry
Database: PDB / ID: 2y7e
TitleCrystal structure of the 3-keto-5-aminohexanoate cleavage enzyme (Kce) from Candidatus Cloacamonas acidaminovorans (tetragonal form)
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
FORMIC ACID / 3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesCANDIDATUS CLOACAMONAS ACIDAMINOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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)62,4237
Polymers62,1762
Non-polymers2475
Water10,539585
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)124,84614
Polymers124,3514
Non-polymers49410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area9670 Å2
ΔGint-199.2 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.188, 102.188, 101.070
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-2181-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0043, 0.9902, 0.1395), (0.9921, -0.0218, 0.1238), (0.1256, 0.1379, -0.9825)
Vector: -8.3055, 1.5603, 50.2494)

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Components

#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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#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.: 585 / 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: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG3350, 0.220 M MG FORMATE, 26.4% GLYCEROL, 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: 1.28→50 Å / Num. obs: 133532 / % possible obs: 97.6 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.4
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0093refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y7D

2y7d


Resolution: 1.28→45.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.145 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 6691 5 %RANDOM
Rwork0.14333 ---
obs0.14465 126786 97.3 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.113 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.28→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 9 585 4817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224413
X-RAY DIFFRACTIONr_bond_other_d0.0010.022997
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9676012
X-RAY DIFFRACTIONr_angle_other_deg0.93837357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85524.175194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96415757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1881532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.487312314
X-RAY DIFFRACTIONr_sphericity_free7.63152
X-RAY DIFFRACTIONr_sphericity_bonded10.78954315
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 396 -
Rwork0.198 7493 -
obs--81.15 %

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