[English] 日本語
Yorodumi
- PDB-6omr: Crystal structure of PtmU3 complexed with PTN substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6omr
TitleCrystal structure of PtmU3 complexed with PTN substrate
ComponentsPtmU3
KeywordsOXIDOREDUCTASE / TIM-barrel
Function / homology
Function and homology information


carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
ACETATE ION / : / Chem-MYM / PtmU3
Similarity search - Component
Biological speciesStreptomyces platensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsLiu, Y.C. / Dong, L.B. / Shen, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114353 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Characterization and Crystal Structure of a Nonheme Diiron Monooxygenase Involved in Platensimycin and Platencin Biosynthesis.
Authors: Dong, L.B. / Liu, Y.C. / Cepeda, A.J. / Kalkreuter, E. / Deng, M.R. / Rudolf, J.D. / Chang, C. / Joachimiak, A. / Phillips Jr., G.N. / Shen, B.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PtmU3
B: PtmU3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,99512
Polymers78,8252
Non-polymers1,17010
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimeric form
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-56 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.620, 122.420, 140.063
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-534-

HOH

21B-667-

HOH

-
Components

#1: Protein PtmU3


Mass: 39412.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces platensis (bacteria) / Plasmid: pRSF/TEV/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A0UVH9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MYM / S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,12alpha)-7-hydroxyatis-16-ene-18-thioate


Mass: 658.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H51N2O9PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.09 Å3/Da / Density % sol: 60.19 % / Mosaicity: 0.47 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Bis-Tris propane pH 7.0, 2.8 M Sodium acetate trihydrate, 4 mM Manganese

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 8, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 36210 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.021 / Rrim(I) all: 0.057 / Χ2: 0.892 / Net I/σ(I): 14.3 / Num. measured all: 267001
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.497.30.8917910.7790.3520.9580.935100
2.49-2.547.30.84517910.8180.3340.9090.947100
2.54-2.597.30.65117970.8660.2580.70.954100
2.59-2.647.40.53617560.9120.2110.5760.934100
2.64-2.77.40.47318070.930.1860.5080.932100
2.7-2.767.40.41117670.9410.1620.4420.902100
2.76-2.837.40.33418050.9580.1320.360.952100
2.83-2.97.40.25418010.9750.10.2730.893100
2.9-2.997.40.19117970.9870.0750.2050.912100
2.99-3.097.40.16217810.9880.0640.1740.89100
3.09-3.27.40.12718160.9940.050.1360.919100
3.2-3.327.40.08718060.9970.0340.0930.927100
3.32-3.487.40.06718030.9980.0260.0720.911100
3.48-3.667.40.0518150.9980.020.0540.92100
3.66-3.897.50.03718150.9990.0150.040.899100
3.89-4.197.40.0318150.9990.0120.0330.887100
4.19-4.617.40.024180710.0090.0250.863100
4.61-5.277.40.02218440.9990.0090.0230.794100
5.27-6.637.30.02118570.9990.0080.0220.729100
6.63-3070.0219390.9980.0090.0220.75399.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OMP

6omp


Resolution: 2.45→29.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.726 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.356 / ESU R Free: 0.265
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 1679 4.8 %RANDOM
Rwork0.182 ---
obs0.1852 33563 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.11 Å2 / Biso mean: 38.853 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.55 Å2
Refinement stepCycle: final / Resolution: 2.45→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 65 321 5932
Biso mean--65.67 35.75 -
Num. residues----712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135756
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175333
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6537873
X-RAY DIFFRACTIONr_angle_other_deg1.3231.58912275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77320.554325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67615870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0421558
X-RAY DIFFRACTIONr_chiral_restr0.0690.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026544
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021284
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 100 -
Rwork0.296 1950 -
all-2050 -
obs--77.71 %

+
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