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- PDB-3a18: Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with... -

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Basic information

Entry
Database: PDB / ID: 3a18
TitleCrystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked crystal)
ComponentsAldoxime dehydratase
KeywordsLYASE / beta barrel / heme protein
Function / homologyaliphatic aldoxime dehydratase / Haem-containing dehydratase / Haem-containing dehydratase / lyase activity / metal ion binding / (1Z)-butanal oxime / PROTOPORPHYRIN IX CONTAINING FE / Aliphatic aldoxime dehydratase
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 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 / 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 / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)171,14512
Polymers168,3314
Non-polymers2,8148
Water15,637868
1
A: Aldoxime dehydratase
B: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5726
Polymers84,1652
Non-polymers1,4074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-50 kcal/mol
Surface area27060 Å2
MethodPISA
2
C: Aldoxime dehydratase
D: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5726
Polymers84,1652
Non-polymers1,4074
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-51 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.118, 148.569, 79.113
Angle α, β, γ (deg.)90.000, 90.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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
111ILEILEPHEPHE1AA5 - 5025 - 70
211ILEILEPHEPHE1CC5 - 5025 - 70
121ASPASPARGARG1AA52 - 34572 - 365
221ASPASPARGARG1CC52 - 34572 - 365
131HEMHEMBXOBXO4AE - F354 - 355
231HEMHEMBXOBXO4CI - J354 - 355
112ILEILEPHEPHE1BB5 - 5025 - 70
212ILEILEPHEPHE1DD5 - 5025 - 70
122ASPASPARGARG1BB52 - 34572 - 365
222ASPASPARGARG1DD52 - 34572 - 365
132HEMHEMBXOBXO4BG - H354 - 355
232HEMHEMBXOBXO4DK - L354 - 355

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-BXO / (1Z)-butanal oxime / n-Butyraldoxime


Mass: 87.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 2.2 Å3/Da / Density % sol: 44.18 % / Mosaicity: 0.46 °
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, 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: 1.8→20 Å / Num. obs: 132895 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.084 / Χ2: 1.187 / Net I/σ(I): 17.235
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.30.288129980.83198
1.86-1.9440.248132430.895199.8
1.94-2.034.20.194133300.996199.9
2.03-2.134.30.152132631.104199.9
2.13-2.274.30.128133041.167199.9
2.27-2.444.40.111133041.2271100
2.44-2.694.40.096132991.3511100
2.69-3.074.50.079133281.479199.9
3.07-3.874.50.062133651.288199.9
3.87-204.60.056134611.334199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A15

3a15


Resolution: 1.8→19.93 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.852 / WRfactor Rfree: 0.282 / WRfactor Rwork: 0.249 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.801 / SU B: 7.653 / SU ML: 0.128 / SU R Cruickshank DPI: 0.186 / SU Rfree: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28 6625 5 %RANDOM
Rwork0.247 ---
obs0.249 132702 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.27 Å2 / Biso mean: 11.456 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11249 0 196 868 12313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02112079
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.97416493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90451459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15223.255642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.621151816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.82515112
X-RAY DIFFRACTIONr_chiral_restr0.0820.21681
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029720
X-RAY DIFFRACTIONr_nbd_refined0.1910.25837
X-RAY DIFFRACTIONr_nbtor_refined0.2960.28084
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.21022
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.232
X-RAY DIFFRACTIONr_mcbond_it0.41.57381
X-RAY DIFFRACTIONr_mcangle_it0.666211516
X-RAY DIFFRACTIONr_scbond_it0.94935468
X-RAY DIFFRACTIONr_scangle_it1.4084.54956
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2621TIGHT POSITIONAL0.060.05
1A49MEDIUM POSITIONAL0.040.5
1A2621TIGHT THERMAL0.070.5
1A49MEDIUM THERMAL0.322
2B2582TIGHT POSITIONAL0.050.05
2B49MEDIUM POSITIONAL0.050.5
2B2582TIGHT THERMAL0.060.5
2B49MEDIUM THERMAL0.342
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 416 -
Rwork0.273 7964 -
all-8380 -
obs--85.31 %
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)
10.5614-0.2893-0.1410.81670.06380.9432-0.0036-0.00660.0021-0.00140.00480.0140.0790.0169-0.0012-0.01480.0037-0.0088-0.03670.006-0.0922-4.429-0.1958.784
20.6443-0.2470.26030.6366-0.18141.3110.0389-0.0049-0.0028-0.0396-0.0164-0.0138-0.16340.0152-0.02250.0081-0.0006-0.003-0.0467-0.003-0.0854-26.79437.1463.465
30.61640.30850.13670.72690.09230.96090.028-0.0162-0.00980.0147-0.0130.0187-0.09370.0084-0.0151-0.0082-0.00240.0017-0.03390.0048-0.091726.99331.05541.823
40.63660.1911-0.31920.5471-0.15921.56340.03440.0239-0.00540.0341-0.0362-0.00160.1687-0.00260.00180.00560.0062-0.0084-0.04490.0011-0.08794.511-6.13247.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 353
2X-RAY DIFFRACTION2B1 - 353
3X-RAY DIFFRACTION3C1 - 353
4X-RAY DIFFRACTION4D1 - 352

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