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- PDB-3a16: Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with... -

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Basic information

Entry
Database: PDB / ID: 3a16
TitleCrystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Propionaldoxime
ComponentsAldoxime dehydratase
KeywordsLYASE / beta barrel / heme protein
Function / homologyaliphatic aldoxime dehydratase / aliphatic aldoxime dehydratase activity / Haem-containing dehydratase / Haem-containing dehydratase / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / (1Z)-propanal oxime / Aliphatic aldoxime dehydratase
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSawai, H. / Sugimoto, H. / Kato, Y. / Asano, Y. / Shiro, Y. / Aono, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: X-ray crystal structure of michaelis complex of aldoxime dehydratase
Authors: Sawai, H. / Sugimoto, H. / Kato, Y. / Asano, Y. / Shiro, Y. / Aono, S.
History
DepositionMar 26, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_alt_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.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_alt_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.pdbx_ptnr1_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldoxime dehydratase
B: Aldoxime dehydratase
C: Aldoxime dehydratase
D: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,13714
Polymers168,3314
Non-polymers2,80710
Water14,970831
1
A: Aldoxime dehydratase
B: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5697
Polymers84,1652
Non-polymers1,4035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-60 kcal/mol
Surface area26970 Å2
MethodPISA
2
C: Aldoxime dehydratase
D: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5697
Polymers84,1652
Non-polymers1,4035
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-57 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.710, 147.670, 78.910
Angle α, β, γ (deg.)90.000, 90.008, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEALAALA3AA5 - 22825 - 248
211ILEILEALAALA3CC5 - 22825 - 248
121GLUGLUARGARG3AA230 - 345250 - 365
221GLUGLUARGARG3CC230 - 345250 - 365
131HEMHEMHEMHEM1AE354
231HEMHEMHEMHEM1CJ354
141PXOPXOPXOPXO6AF355
241PXOPXOPXOPXO6CK355
112ILEILEALAALA3BB5 - 22825 - 248
212ILEILEALAALA3DD5 - 22825 - 248
122GLUGLUARGARG3BB230 - 345250 - 365
222GLUGLUARGARG3DD230 - 345250 - 365
132HEMHEMHEMHEM1BG354
232HEMHEMHEMHEM1DL354
142PXOPXOPXOPXO6BH355
242PXOPXOPXOPXO6DM355

NCS ensembles :
ID
1
2

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Components

#1: Protein
Aldoxime dehydratase / OxdRE


Mass: 42082.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: oxd / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76K71, EC: 4.99.1.5
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-PXO / (1Z)-propanal oxime / (Z)-propionaldoxime


Mass: 73.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 831 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 18% (W/V) PEG 4000, 0.075M sodium cacodylate, 0.1M magnesium acetate; crystal was soaked into propionaldoxime, pH 7.4, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 188090 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 22.651 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.4
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 10 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 8.1 / Num. measured obs: 137927 / Num. unique obs: 13912 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A15

3a15


Resolution: 1.6→19.81 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.257 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 5.317 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 9497 5 %RANDOM
Rwork0.248 ---
obs0.25 188090 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.88 Å2 / Biso mean: 10.508 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å2-0.22 Å2
2---1.47 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11674 0 194 831 12699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02112226
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.97316687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02151470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58623.302645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.454151833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.80415109
X-RAY DIFFRACTIONr_chiral_restr0.0870.21703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029827
X-RAY DIFFRACTIONr_nbd_refined0.1890.25827
X-RAY DIFFRACTIONr_nbtor_refined0.2970.28197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2996
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.230
X-RAY DIFFRACTIONr_mcbond_it0.51.57493
X-RAY DIFFRACTIONr_mcangle_it0.762211684
X-RAY DIFFRACTIONr_scbond_it1.22835509
X-RAY DIFFRACTIONr_scangle_it1.6884.54990
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1394TIGHT POSITIONAL0.030.05
1A1345LOOSE POSITIONAL0.245
1A1394TIGHT THERMAL0.110.5
1A1345LOOSE THERMAL0.710
2B1494TIGHT POSITIONAL0.030.05
2B1454LOOSE POSITIONAL0.275
2B1494TIGHT THERMAL0.10.5
2B1454LOOSE THERMAL0.6710
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.6410.3147190.268130961381699.993
1.641-1.6860.3137380.2711275013488100
1.686-1.7340.3146700.2681241413084100
1.734-1.7870.3016340.2661217312807100
1.787-1.8460.316040.2621169512299100
1.846-1.910.3085660.2571132811894100
1.91-1.9810.2915960.2521094811544100
1.981-2.0610.2875650.2421051811083100
2.061-2.1520.2765480.2451014110689100
2.152-2.2550.2795240.246965110175100
2.255-2.3760.2674800.2592089688100
2.376-2.5180.2794700.25487589228100
2.518-2.6880.2823880.2581968584100
2.688-2.8990.2654050.24976628067100
2.899-3.1690.2673610.2467099746199.987
3.169-3.5320.2573340.23964006734100
3.532-4.0570.2383150.235661597899.967
4.057-4.9170.2222450.234863511799.824
4.917-6.750.2692170.2493810403099.926
6.75-19.8150.2861180.2672222246295.045

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