[English] 日本語
Yorodumi
- PDB-3a16: Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with... -

+
Open data


ID or keywords:

Loading...

-
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 / Haem-containing dehydratase / Haem-containing dehydratase / lyase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more