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- PDB-3a15: Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase ... -

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Basic information

Entry
Database: PDB / ID: 3a15
TitleCrystal Structure of Substrate-Free Form of Aldoxime Dehydratase (OxdRE)
ComponentsAldoxime dehydratase
KeywordsLYASE / beta barrel / heme protein
Function / homologyaliphatic aldoxime dehydratase / Haem-containing dehydratase / Haem-containing dehydratase / lyase activity / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Aliphatic aldoxime dehydratase
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 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 / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
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 / struct_conn / 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_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

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)170,7968
Polymers168,3314
Non-polymers2,4664
Water23,4011299
1
A: Aldoxime dehydratase
B: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3984
Polymers84,1652
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-50 kcal/mol
Surface area27810 Å2
MethodPISA
2
C: Aldoxime dehydratase
D: Aldoxime dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3984
Polymers84,1652
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-49 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.904, 77.066, 104.831
Angle α, β, γ (deg.)90.000, 101.060, 90.000
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1299 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.66 % / Mosaicity: 0.869 °
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU21.7379, 1.7404, 1.7200
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 6, 2008
ADSC QUANTUM 3152CCDFeb 6, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.73791
31.74041
41.721
ReflectionRedundancy: 5 % / Av σ(I) over netI: 22.83 / Number: 385356 / Rmerge(I) obs: 0.083 / Χ2: 0.95 / D res high: 2.2 Å / D res low: 20 Å / Num. obs: 77303 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.722099.910.0631.0675.3
3.764.7299.410.0670.9954.9
3.283.7699.410.0780.9735.1
2.983.2899.510.0841.0715.1
2.772.9899.510.0930.9085.1
2.612.7799.810.1080.8485.1
2.482.6199.510.1390.9915.1
2.372.4899.910.1620.9794.9
2.282.3799.610.1930.884.7
2.22.2899.110.210.84.4
ReflectionResolution: 1.79→20 Å / Num. obs: 141582 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Χ2: 0.97 / Net I/σ(I): 22.83
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.79-1.862.80.3252.6139380.61298.7
1.86-1.942.80.231140000.62999.1
1.94-2.034.20.22141260.67899.7
2.03-2.134.60.183141360.96699.9
2.13-2.274.70.13141690.85199.9
2.27-2.444.80.107141500.95399.9
2.44-2.694.90.088141671.24399.9
2.69-3.0750.075142101.25699.8
3.07-3.874.90.048142381.06799.7
3.87-205.40.036144480.98699.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→19.88 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.017 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 7085 5 %RANDOM
Rwork0.161 ---
obs0.163 141557 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.21 Å2 / Biso mean: 29.25 Å2 / Biso min: 13.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.37 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.79→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11376 0 172 1299 12847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02111999
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.97316393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00651454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81423.281637
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55151809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.25515111
X-RAY DIFFRACTIONr_chiral_restr0.0930.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029651
X-RAY DIFFRACTIONr_nbd_refined0.1930.25581
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.21167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.249
X-RAY DIFFRACTIONr_mcbond_it0.6491.57369
X-RAY DIFFRACTIONr_mcangle_it1.033211475
X-RAY DIFFRACTIONr_scbond_it1.635403
X-RAY DIFFRACTIONr_scangle_it2.4874.54896
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 (%)
1.794-1.840.2454680.20388351048988.693
1.84-1.890.2354950.18595931019398.97
1.89-1.9450.2264880.1769351994098.984
1.945-2.0040.1984970.1679100961899.782
2.004-2.0690.1934610.1658891935999.925
2.069-2.1410.2094540.1668605906699.923
2.141-2.220.2154120.1638312873199.92
2.22-2.310.1954140.1618006842799.917
2.31-2.4110.2064020.177672808399.889
2.411-2.5270.1983970.1727316772199.896
2.527-2.6610.2073860.1726992739399.797
2.661-2.820.2123550.1716615698199.842
2.82-3.010.1823150.1726248657999.757
3.01-3.2450.1893290.1655806614399.87
3.245-3.5460.1732730.155373565499.859
3.546-3.9490.1682790.1394854518099.093
3.949-4.530.1552360.1354329457099.891
4.53-5.4780.1972010.1443729393199.975
5.478-7.4720.2181420.1812971311499.968
7.472-200.171810.1731874196899.339
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)
10.6703-0.0704-0.00930.16550.11260.3672-0.0099-0.05650.01720.01450.0299-0.00970.00510.0346-0.0201-0.02510.00250.0062-0.04960.002-0.0135-3.47319.35366.723
20.75880.13810.2920.42610.1090.3345-0.02070.00360.0114-0.02140.01380.0384-0.0078-0.00530.0069-0.0370.00020.0022-0.06730.00210.0006-43.45621.37449.271
30.987-0.0306-0.3960.28750.08211.4027-0.0356-0.10110.0102-0.03160.0662-0.02560.14370.1397-0.03050.00520.03480.0523-0.0490.0251-0.0808-8.482-15.48191.227
41.0870.00890.1770.8333-0.07061.1512-0.0209-0.06330.0439-0.21240.01320.09640.0973-0.23010.0077-0.0228-0.0488-0.04540.04260.0101-0.1024-52.347-16.64492.902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 352
2X-RAY DIFFRACTION2B-9 - 352
3X-RAY DIFFRACTION3C1 - 352
4X-RAY DIFFRACTION4D-9 - 352

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