[English] 日本語
Yorodumi
- PDB-5kox: Structure of rifampicin monooxygenase complexed with rifampicin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kox
TitleStructure of rifampicin monooxygenase complexed with rifampicin
ComponentsPentachlorophenol 4-monooxygenase
KeywordsOXIDOREDUCTASE / flavoprotein / monooxygenase
Function / homology
Function and homology information


pentachlorophenol monooxygenase / pentachlorophenol monooxygenase activity / rifampicin monooxygenase / FAD binding / monooxygenase activity
Similarity search - Function
Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin ...Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / RIFAMPICIN / Pentachlorophenol 4-monooxygenase / Rifampicin monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTanner, J.J. / Liu, L.-K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1506206 United States
National Science Foundation (NSF, United States)MCB-1021384 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Structure of the Antibiotic Deactivating, N-hydroxylating Rifampicin Monooxygenase.
Authors: Liu, L.K. / Abdelwahab, H. / Martin Del Campo, J.S. / Mehra-Chaudhary, R. / Sobrado, P. / Tanner, J.J.
History
DepositionJul 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pentachlorophenol 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3263
Polymers51,7181
Non-polymers1,6082
Water2,918162
1
A: Pentachlorophenol 4-monooxygenase
hetero molecules

A: Pentachlorophenol 4-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,6526
Polymers103,4352
Non-polymers3,2174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area7870 Å2
ΔGint-53 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.439, 81.439, 287.354
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-682-

HOH

-
Components

#1: Protein Pentachlorophenol 4-monooxygenase


Mass: 51717.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (bacteria) / Gene: pcpB_1, ERS450000_00511 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0H5NE66, UniProt: Q5YTV5*PLUS, pentachlorophenol monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-RFP / RIFAMPICIN / Rifampicin


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The reservoir contained 17% (w/v) PEG 3350, 200 mM magnesium chloride, and 2.5% glycerol. The protein stock solution included 5 mM rifampicin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→57.47 Å / Num. obs: 97168 / % possible obs: 98.4 % / Redundancy: 18.8 % / Biso Wilson estimate: 17.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 36.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.8412.80.4530.884183.9
9-57.4715.10.0271198.3

-
Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX(1.10_2155)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k2x

4k2x


Resolution: 1.8→56.793 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.9
RfactorNum. reflection% reflection
Rfree0.2151 3707 3.82 %
Rwork0.1796 --
obs0.181 97168 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.11 Å2 / Biso mean: 21.4772 Å2 / Biso min: 8.03 Å2
Refinement stepCycle: final / Resolution: 1.8→56.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 105 162 3881
Biso mean--18.46 21.57 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153809
X-RAY DIFFRACTIONf_angle_d1.515197
X-RAY DIFFRACTIONf_chiral_restr0.087579
X-RAY DIFFRACTIONf_plane_restr0.01676
X-RAY DIFFRACTIONf_dihedral_angle_d17.12213
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82370.24821200.22013021314182
1.8237-1.84870.26271250.20363149327485
1.8487-1.87510.24611280.18983292342092
1.8751-1.90310.24391410.18293609375097
1.9031-1.93280.21161460.186836603806100
1.9328-1.96450.25471480.187536053753100
1.9645-1.99840.22851430.187436793822100
1.9984-2.03470.23411470.18436803827100
2.0347-2.07390.25851450.186536463791100
2.0739-2.11620.22741440.184236243768100
2.1162-2.16220.2311450.180136673812100
2.1622-2.21250.19091420.178136573799100
2.2125-2.26790.26951410.180336723813100
2.2679-2.32920.2741440.1836553799100
2.3292-2.39770.22361450.180736793824100
2.3977-2.47510.25111460.186236503796100
2.4751-2.56360.21751440.18736513795100
2.5636-2.66620.24331490.196536373786100
2.6662-2.78750.26141450.192336313776100
2.7875-2.93450.21491420.197936793821100
2.9345-3.11830.21451510.204536703821100
3.1183-3.35910.21781450.195636483793100
3.3591-3.69710.20561480.176536573805100
3.6971-4.23190.16411450.158936353780100
4.2319-5.33110.15551500.143836513801100
5.3311-56.82160.18851380.153636573795100
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)
10.9181-0.02480.23461.12880.32230.5499-0.0051-0.04940.1567-0.0317-0.05290.1409-0.0589-0.07360.05650.11480.025-0.00410.105-0.0180.13032.951836.1431-11.0128
21.3866-0.75170.04651.679-0.821.63990.17520.16990.1312-0.2253-0.1031-0.03190.02720.1199-0.07370.19090.04470.02460.16070.0140.146518.390335.2516-34.5442
30.7532-0.3134-0.45680.95170.56310.8925-0.0359-0.0787-0.01370.0657-0.00260.04450.07570.00760.03520.11840.0267-0.00440.09970.00570.09639.207922.1454-11.7386
42.07870.4732-0.3081.31410.2461.9715-0.0596-0.1239-0.28220.1958-0.02380.24310.2317-0.03970.05760.1790.02180.05330.1331-0.00320.2369-12.402517.0162-0.8865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 170 )A1 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 258 )A171 - 258
3X-RAY DIFFRACTION3chain 'A' and (resid 259 through 377 )A259 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 473 )A378 - 473

+
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