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- PDB-3axg: Structure of 6-aminohexanoate-oligomer hydrolase -

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Basic information

Entry
Database: PDB / ID: 3axg
TitleStructure of 6-aminohexanoate-oligomer hydrolase
ComponentsEndotype 6-aminohexanoat-oligomer hydrolase
KeywordsHYDROLASE / Nylon oligomer
Function / homologyPeptidase S58, DmpA / Peptidase family S58 / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / aminopeptidase activity / 4-Layer Sandwich / Alpha Beta / Endotype 6-aminohexanoat-oligomer hydrolase
Function and homology information
Biological speciesAgromyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsNegoro, S. / Shibata, N. / Tanaka, Y. / Yasuhira, K. / Shibata, H. / Hashimoto, H. / Lee, Y.H. / Ohshima, S. / Santa, R. / Mochiji, K. ...Negoro, S. / Shibata, N. / Tanaka, Y. / Yasuhira, K. / Shibata, H. / Hashimoto, H. / Lee, Y.H. / Ohshima, S. / Santa, R. / Mochiji, K. / Goto, Y. / Ikegami, T. / Nagai, K. / Kato, D. / Takeo, M. / Higuchi, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Three-dimensional structure of nylon hydrolase and mechanism of nylon-6 hydrolysis
Authors: Negoro, S. / Shibata, N. / Tanaka, Y. / Yasuhira, K. / Shibata, H. / Hashimoto, H. / Lee, Y.H. / Oshima, S. / Santa, R. / Mochiji, K. / Goto, Y. / Ikegami, T. / Nagai, K. / Kato, D. / Takeo, M. / Higuchi, Y.
History
DepositionApr 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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: Endotype 6-aminohexanoat-oligomer hydrolase
B: Endotype 6-aminohexanoat-oligomer hydrolase
C: Endotype 6-aminohexanoat-oligomer hydrolase
D: Endotype 6-aminohexanoat-oligomer hydrolase
E: Endotype 6-aminohexanoat-oligomer hydrolase
F: Endotype 6-aminohexanoat-oligomer hydrolase
G: Endotype 6-aminohexanoat-oligomer hydrolase
H: Endotype 6-aminohexanoat-oligomer hydrolase
I: Endotype 6-aminohexanoat-oligomer hydrolase
J: Endotype 6-aminohexanoat-oligomer hydrolase
K: Endotype 6-aminohexanoat-oligomer hydrolase
L: Endotype 6-aminohexanoat-oligomer hydrolase
M: Endotype 6-aminohexanoat-oligomer hydrolase
N: Endotype 6-aminohexanoat-oligomer hydrolase
O: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)554,03221
Polymers553,89415
Non-polymers1386
Water51,4512856
1
A: Endotype 6-aminohexanoat-oligomer hydrolase
B: Endotype 6-aminohexanoat-oligomer hydrolase
C: Endotype 6-aminohexanoat-oligomer hydrolase
D: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7285
Polymers147,7054
Non-polymers231
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18520 Å2
ΔGint-116 kcal/mol
Surface area39710 Å2
MethodPISA
2
E: Endotype 6-aminohexanoat-oligomer hydrolase
F: Endotype 6-aminohexanoat-oligomer hydrolase
G: Endotype 6-aminohexanoat-oligomer hydrolase
H: Endotype 6-aminohexanoat-oligomer hydrolase


Theoretical massNumber of molelcules
Total (without water)147,7054
Polymers147,7054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18510 Å2
ΔGint-115 kcal/mol
Surface area39600 Å2
MethodPISA
3
I: Endotype 6-aminohexanoat-oligomer hydrolase
J: Endotype 6-aminohexanoat-oligomer hydrolase
K: Endotype 6-aminohexanoat-oligomer hydrolase
L: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7516
Polymers147,7054
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18490 Å2
ΔGint-117 kcal/mol
Surface area39840 Å2
MethodPISA
4
M: Endotype 6-aminohexanoat-oligomer hydrolase
N: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules

M: Endotype 6-aminohexanoat-oligomer hydrolase
N: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7978
Polymers147,7054
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area18460 Å2
ΔGint-113 kcal/mol
Surface area39840 Å2
MethodPISA
5
O: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules

O: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules

O: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules

O: Endotype 6-aminohexanoat-oligomer hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,7978
Polymers147,7054
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area18630 Å2
ΔGint-115 kcal/mol
Surface area39450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.863, 214.446, 478.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
Endotype 6-aminohexanoat-oligomer hydrolase / Nylon oligomers-degrading enzyme EIII


Mass: 36926.238 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agromyces (bacteria) / Strain: KY5R / Gene: nylC / Plasmid: pBluescript II SK(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q1EPR5
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2856 / 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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.0M SODIUM CITRATE, 0.2M SODIUM CHLORIDE, 0.1M HEPES BUFFER(PH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 18, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 501977 / Num. obs: 501977 / % possible obs: 94.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.32 / % possible all: 73

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Processing

Software
NameVersionClassification
BSSdata collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→49.99 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 241679.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.24 50323 10 %RANDOM
Rwork0.211 ---
obs0.211 501977 94.1 %-
all-501977 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.7725 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.39 Å20 Å20 Å2
2--5.52 Å20 Å2
3----1.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→49.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37819 0 6 2856 40681
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 3856 10.3 %
Rwork0.318 33528 -
obs--70.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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