[English] 日本語
Yorodumi
- PDB-4xbz: Crystal Structure of EvdO1 from Micromonospora carbonacea var. au... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xbz
TitleCrystal Structure of EvdO1 from Micromonospora carbonacea var. aurantiaca
ComponentsEvdO1
KeywordsOXIDOREDUCTASE / double stranded beta helix
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / NICKEL (II) ION / EvdO1
Function and homology information
Biological speciesMicromonospora carbonacea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMcCulloch, K.M. / McCranie, E.K. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oxidative cyclizations in orthosomycin biosynthesis expand the known chemistry of an oxygenase superfamily.
Authors: McCulloch, K.M. / McCranie, E.K. / Smith, J.A. / Sarwar, M. / Mathieu, J.L. / Gitschlag, B.L. / Du, Y. / Bachmann, B.O. / Iverson, T.M.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _pdbx_struct_oper_list.symmetry_operation / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EvdO1
B: EvdO1
C: EvdO1
D: EvdO1
E: EvdO1
F: EvdO1
G: EvdO1
H: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,73022
Polymers300,7088
Non-polymers1,02214
Water24,0141333
1
A: EvdO1
B: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4796
Polymers75,1772
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-35 kcal/mol
Surface area25550 Å2
MethodPISA
2
C: EvdO1
D: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3865
Polymers75,1772
Non-polymers2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-31 kcal/mol
Surface area26170 Å2
MethodPISA
3
E: EvdO1
F: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3865
Polymers75,1772
Non-polymers2093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-28 kcal/mol
Surface area25350 Å2
MethodPISA
4
G: EvdO1
H: EvdO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4796
Polymers75,1772
Non-polymers3024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-36 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.615, 109.432, 146.050
Angle α, β, γ (deg.)90.000, 108.270, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. There are 4 biological units in the asymmetric unit (chains A & B, chains C & D, chains E & F, and chains G & H).

-
Components

#1: Protein
EvdO1


Mass: 37588.465 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora carbonacea (bacteria) / Strain: var. aurantiaca / Gene: evdO1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL03*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1333 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe authors state that the structure contains four dimers in the ASU and four partially ordered ...The authors state that the structure contains four dimers in the ASU and four partially ordered purification His tags, of which it is unclear what chain the tag belongs to. They are currently modeled as part of the polymer chains.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 100 mM sodium citrate, 13% PEG8000, crystals soaked with 2 mM NiCl2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.979
SYNCHROTRONAPS 21-ID-D21.485
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.4851
ReflectionRedundancy: 7.7 % / Number: 462649 / Rmerge(I) obs: 0.121 / Χ2: 1.95 / D res high: 2.9 Å / D res low: 50 Å / Num. obs: 60108 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
7.865010.052.9067.3
6.247.8610.0662.3467.6
5.466.2410.0752.2567.7
4.965.4610.0782.3567.6
4.64.9610.0782.577.7
4.334.610.0842.5857.6
4.114.3310.0922.4887.7
3.944.1110.1032.3617.7
3.783.9410.1162.37.7
3.653.7810.1342.1867.7
3.543.6510.1441.9357.7
3.443.5410.1571.8227.7
3.353.4410.1811.7687.8
3.273.3510.2061.5967.8
3.193.2710.2411.4337.8
3.123.1910.2781.347.8
3.063.1210.2971.37.8
33.0610.3411.1987.8
2.95310.3861.1747.8
2.92.9510.4181.1377.8
ReflectionResolution: 2.3→50 Å / Num. obs: 120971 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.051 / Rrim(I) all: 0.101 / Χ2: 1.019 / Net I/av σ(I): 15.212 / Net I/σ(I): 7.5 / Num. measured all: 456961
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.10.44359730.7880.3010.5380.81499.1
2.34-2.383.30.41459990.8230.2730.4980.84899.2
2.38-2.433.50.36360210.8850.230.4310.84399.2
2.43-2.483.80.33360200.9220.1980.3880.8699.3
2.48-2.533.90.30459780.9350.1780.3520.84799.4
2.53-2.593.90.26360090.9480.1540.3050.86699.4
2.59-2.663.90.2260390.970.1290.2560.86899.5
2.66-2.733.90.21660290.9620.1260.250.92199.5
2.73-2.813.90.17260630.9750.1010.1990.89899.5
2.81-2.93.90.14960070.980.0870.1730.93199.6
2.9-33.90.1360070.9830.0760.1511.00799.7
3-3.123.90.11560600.9870.0670.1331.10799.7
3.12-3.263.90.10560670.9860.0620.1221.2399.7
3.26-3.443.90.08860740.9880.0520.1021.39199.7
3.44-3.653.90.07360890.9910.0430.0851.31399.8
3.65-3.933.90.06260390.9930.0360.0711.28799.8
3.93-4.333.90.05460980.9950.0320.0631.23899.8
4.33-4.953.90.05360820.9950.0310.0621.34399.8
4.95-6.243.90.0561120.9940.030.0581.10499.8
6.24-503.70.03662050.9980.0210.0420.51399.3

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→46.316 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 6079 5.03 %
Rwork0.183 114814 -
obs0.1857 120893 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 35.2407 Å2 / Biso min: 16.41 Å2
Refinement stepCycle: final / Resolution: 2.3→46.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19105 0 44 1333 20482
Biso mean--44.25 38.45 -
Num. residues----2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819634
X-RAY DIFFRACTIONf_angle_d1.07126778
X-RAY DIFFRACTIONf_chiral_restr0.0412889
X-RAY DIFFRACTIONf_plane_restr0.0063528
X-RAY DIFFRACTIONf_dihedral_angle_d14.5797220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2993-2.32550.32161590.23273699385895
2.3255-2.35280.31472250.23463805403099
2.3528-2.38150.29162310.22493732396399
2.3815-2.41170.32812060.22263839404599
2.4117-2.44340.28541900.21843777396799
2.4434-2.47690.27992150.21493806402199
2.4769-2.51220.27462040.21013808401299
2.5122-2.54970.29392250.20953814403999
2.5497-2.58960.30111800.20753745392599
2.5896-2.6320.31572070.21323868407599
2.632-2.67740.27351990.20013800399999
2.6774-2.72610.29152050.205638134018100
2.7261-2.77850.27631950.204338134008100
2.7785-2.83520.29891830.203438454028100
2.8352-2.89690.27362020.205238604062100
2.8969-2.96420.25722130.200838214034100
2.9642-3.03840.27351840.206538544038100
3.0384-3.12050.29211960.20837993995100
3.1205-3.21230.26112360.204738074043100
3.2123-3.31590.24022070.194338474054100
3.3159-3.43440.25081680.181838774045100
3.4344-3.57190.23772240.177338194043100
3.5719-3.73440.21451820.165238434025100
3.7344-3.93120.19072020.158138694071100
3.9312-4.17730.18252040.150338674071100
4.1773-4.49960.18592230.149238054028100
4.4996-4.9520.18622090.143438914100100
4.952-5.66740.17572020.160338694071100
5.6674-7.13610.24591960.180739004096100
7.1361-46.32510.19922070.17833922412999

+
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://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