[English] 日本語
Yorodumi
- PDB-2rdr: Crystal Structure of PtlH with Fe/oxalylglycine bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rdr
TitleCrystal Structure of PtlH with Fe/oxalylglycine bound
Components1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase
KeywordsOXIDOREDUCTASE / double stranded barrel helix / dioxygenase
Function / homology
Function and homology information


1-deoxypentalenic acid 11beta-hydroxylase / lactone biosynthetic process / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / 1-deoxypentalenic acid 11-beta-hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsYou, Z. / Omura, S. / Ikeda, H. / Cane, D.E. / Jogl, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal Structure of the Non-heme Iron Dioxygenase PtlH in Pentalenolactone Biosynthesis.
Authors: You, Z. / Omura, S. / Ikeda, H. / Cane, D.E. / Jogl, G.
History
DepositionSep 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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 / _struct_conn.pdbx_dist_value / _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_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_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: 1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8164
Polymers32,5891
Non-polymers2273
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.769, 70.564, 48.023
Angle α, β, γ (deg.)90.000, 113.170, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 1-deoxypentalenic acid 11-beta hydroxylase; Fe(II)/alpha-ketoglutarate dependent hydroxylase


Mass: 32588.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: ptlH / Plasmid: pET28e / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82IZ1
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 282 K / Method: sitting drop / pH: 7.5
Details: 100mM HEPES, 200mM MgCl2, 20% PEG 3350, pH 7.5, sitting drop, temperature 282K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 26, 2006
RadiationMonochromator: Rigaku Osmic Confocal Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 30519 / % possible obs: 98.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.076 / Χ2: 1.088 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.762.40.52430641.1251100
1.76-1.832.40.40230931.231100
1.83-1.912.40.30730861.1481100
1.91-2.022.50.21930721.08199.9
2.02-2.142.50.16630721.078199.7
2.14-2.312.50.12430771.088199.3
2.31-2.542.60.09630571.047198.9
2.54-2.912.60.0730401.053197.9
2.91-3.662.70.04130081.075196.8
3.66-302.70.02929500.984193.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.5 / Cor.coef. Fo:Fc: 51.95
Highest resolutionLowest resolution
Rotation4 Å10 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMO1.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.081 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1537 5 %RANDOM
Rwork0.174 ---
obs0.176 30496 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.24 Å2
2---0.11 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 12 448 2583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212243
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9453055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.59223.043115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.871518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021790
X-RAY DIFFRACTIONr_nbd_refined0.2040.21170
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2422
X-RAY DIFFRACTIONr_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.231
X-RAY DIFFRACTIONr_mcbond_it0.631.51384
X-RAY DIFFRACTIONr_mcangle_it0.97522195
X-RAY DIFFRACTIONr_scbond_it1.7283964
X-RAY DIFFRACTIONr_scangle_it2.694.5860
LS refinement shellResolution: 1.7→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 109 -
Rwork0.307 2074 -
all-2183 -
obs--96.59 %
Refinement TLS params.Method: refined / Origin x: 4.6492 Å / Origin y: 0.0047 Å / Origin z: 17.4981 Å
111213212223313233
T-0.0213 Å20.0076 Å20.0027 Å2--0.0148 Å20.0022 Å2---0.0157 Å2
L0.2892 °2-0.0938 °2-0.0641 °2-0.3196 °20.0443 °2--0.2771 °2
S0.0141 Å °0.019 Å °0.0054 Å °-0.022 Å °-0.0206 Å °0.0202 Å °-0.0066 Å °0.0008 Å °0.0066 Å °

+
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