[English] 日本語
Yorodumi
- PDB-3sdo: Structure of a Nitrilotriacetate monooxygenase from Burkholderia ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sdo
TitleStructure of a Nitrilotriacetate monooxygenase from Burkholderia pseudomallei
ComponentsNitrilotriacetate monooxygenase
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity
Similarity search - Function
Nitrilotriacetate monooxygenase component A/pristinamycin IIA synthase subunit A / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Nitrilotriacetate monooxygenase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of a Nitrilotriacetate monooxygenase from Burkholderia pseudomallei
Authors: Clifton, M.C. / Edwards, T.E. / Seattle Structural Genomics Center for Infectious Disease / Sankaran, B.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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_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_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: Nitrilotriacetate monooxygenase
B: Nitrilotriacetate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5395
Polymers99,3532
Non-polymers1863
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-25 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.187, 92.783, 162.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Nitrilotriacetate monooxygenase


Mass: 49676.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A1398 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JIP8, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 43.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium acetate, 0.1 M Bis Tris Propane, pH 7.5, 20% PEG3350. 38.61 mg/mL. Cryoprotection 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.997→48.683 Å / Num. all: 59660 / Num. obs: 56755 / % possible obs: 99.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.006 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.983.10.36862470.923199.9
1.98-2.023.20.34261740.9421100
2.02-2.063.20.29161921.0011100
2.06-2.13.20.26261931.063199.9
2.1-2.153.30.22661601.0481100
2.15-2.23.30.19762441.0741100
2.2-2.253.30.1861351.0531100
2.25-2.313.30.16162341.077199.9
2.31-2.383.30.14262331.066199.9
2.38-2.463.30.13261691.058199.9
2.46-2.543.30.11962181.0471100
2.54-2.653.30.10762241.0411100
2.65-2.773.30.09861940.9751100
2.77-2.913.30.08762420.969199.9
2.91-3.13.30.08162440.922199.8
3.1-3.333.30.07662290.972199.4
3.33-3.673.30.07161390.95198
3.67-4.23.20.06561230.914197.3
4.2-5.293.20.05362251.081198.4
5.29-503.30.03563800.948197.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.68 Å
Translation2.5 Å48.68 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YW1

1yw1


Resolution: 2→48.683 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2092 / WRfactor Rwork: 0.1737 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8771 / SU B: 7.58 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1816 / SU Rfree: 0.1572 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2887 5.1 %RANDOM
Rwork0.172 ---
obs0.1741 56755 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.74 Å2 / Biso mean: 27.3102 Å2 / Biso min: 5.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--1.69 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2→48.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6368 0 12 490 6870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216553
X-RAY DIFFRACTIONr_bond_other_d0.0010.024410
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.948912
X-RAY DIFFRACTIONr_angle_other_deg0.867310599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5545839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42722.564312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51615922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6261560
X-RAY DIFFRACTIONr_chiral_restr0.0790.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021486
X-RAY DIFFRACTIONr_mcbond_it0.6571.54169
X-RAY DIFFRACTIONr_mcbond_other0.1571.51706
X-RAY DIFFRACTIONr_mcangle_it1.1926621
X-RAY DIFFRACTIONr_scbond_it1.84432384
X-RAY DIFFRACTIONr_scangle_it2.9864.52289
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 211 -
Rwork0.199 3752 -
all-3963 -
obs--90.58 %
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)
10.50920.0647-0.02910.4893-0.1880.6886-0.00560.0271-0.0746-0.0444-0.0034-0.07030.06510.08640.0090.0760.02120.00650.0948-0.02230.051350.596883.649724.2615
20.395-0.04330.05380.27990.02030.6648-0.02140.0976-0.0605-0.0490.0222-0.00530.1316-0.0272-0.00080.08140.01620.00690.0641-0.01840.074342.238676.460519.4191
32.84461.36230.89354.31380.45452.44250.08370.01180.013-0.2371-0.24040.34430.2282-0.21890.15670.05250.0022-0.00770.151-0.0810.060776.332983.28172.6169
40.53150.0513-0.03630.5116-0.26541.0170.01710.0690.00810.0023-0.0058-0.0206-0.00480.016-0.01140.09810.0203-0.00360.1197-0.01590.053742.245490.19999.8787
50.9465-0.0539-0.16670.34290.17151.0765-0.0095-0.0768-0.15730.0653-0.0117-0.00860.1280.02410.02120.10390.0151-0.00230.09140.01780.061642.155380.389146.2712
60.5998-0.1185-0.41430.27030.13141.2625-0.0687-0.1467-0.06260.09370.0028-0.01170.19150.1850.06590.08540.0185-0.02030.11680.01010.061155.019180.094451.5597
73.97394.3632-0.261911.6812-0.29984.5241-0.0968-0.0987-0.2538-0.271-0.051-0.4254-0.04850.20260.14780.2670.06950.03610.29530.0620.230925.37566.51564.34
80.3744-0.1511-0.49020.0910.19521.16930.0193-0.0910.01290.03820.0153-0.0166-0.06870.1142-0.03460.0942-0.0048-0.02040.095-0.0130.026146.380991.338861.1419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2A148 - 298
3X-RAY DIFFRACTION3A299 - 358
4X-RAY DIFFRACTION4A359 - 441
5X-RAY DIFFRACTION5B3 - 146
6X-RAY DIFFRACTION6B147 - 293
7X-RAY DIFFRACTION7B294 - 366
8X-RAY DIFFRACTION8B367 - 441

+
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