[English] 日本語
Yorodumi
- PDB-5bk7: The structure of MppP E15A mutant soaked with the substrate L-arginine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bk7
TitleThe structure of MppP E15A mutant soaked with the substrate L-arginine
ComponentsPLP-Dependent L-Arginine Hydroxylase MppP
KeywordsOXIDOREDUCTASE / dimer / substrate binding in E15A mutant / oxidase / PLP / hydrolase-antibiotic complex
Function / homology
Function and homology information


amino acid metabolic process / transaminase activity / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
Enduracididine biosynthesis enzyme MppP / : / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Enduracididine biosynthesis enzyme MppP / : / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EQJ / Class I and II aminotransferase
Similarity search - Component
Biological speciesStreptomyces wadayamensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å
AuthorsHan, L. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1606842 United States
CitationJournal: Biochemistry / Year: 2018
Title: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Authors: Han, L. / Vuksanovic, N. / Oehm, S.A. / Fenske, T.G. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionJan 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
E: PLP-Dependent L-Arginine Hydroxylase MppP
F: PLP-Dependent L-Arginine Hydroxylase MppP
G: PLP-Dependent L-Arginine Hydroxylase MppP
H: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,06416
Polymers331,8388
Non-polymers3,2278
Water15,241846
1
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-32 kcal/mol
Surface area25050 Å2
MethodPISA
2
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-30 kcal/mol
Surface area25210 Å2
MethodPISA
3
E: PLP-Dependent L-Arginine Hydroxylase MppP
F: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-31 kcal/mol
Surface area25070 Å2
MethodPISA
4
G: PLP-Dependent L-Arginine Hydroxylase MppP
H: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7664
Polymers82,9592
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-31 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.441, 200.514, 139.930
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PLP-Dependent L-Arginine Hydroxylase MppP


Mass: 41479.719 Da / Num. of mol.: 8 / Mutation: E15A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#2: Chemical
ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine


Mass: 403.328 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H22N5O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.04 M citric acid, 0.06 M BIS-TRIS Propane, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 170041 / % possible obs: 97 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 7831 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1

5dj1


Resolution: 2.196→45.401 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2001 1.28 %
Rwork0.2008 --
obs0.2015 156244 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.196→45.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22848 0 216 846 23910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01323552
X-RAY DIFFRACTIONf_angle_d1.30832075
X-RAY DIFFRACTIONf_dihedral_angle_d19.46513997
X-RAY DIFFRACTIONf_chiral_restr0.0673634
X-RAY DIFFRACTIONf_plane_restr0.0084209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1956-2.25050.3571910.29616483X-RAY DIFFRACTION53
2.2505-2.31130.30681120.27658365X-RAY DIFFRACTION68
2.3113-2.37930.32921230.26819550X-RAY DIFFRACTION77
2.3793-2.45610.30671270.261210297X-RAY DIFFRACTION83
2.4561-2.54390.35331410.259710999X-RAY DIFFRACTION89
2.5439-2.64570.31771530.25311715X-RAY DIFFRACTION95
2.6457-2.76610.28211510.251112059X-RAY DIFFRACTION98
2.7661-2.91190.35351630.238112098X-RAY DIFFRACTION97
2.9119-3.09440.29261530.231211631X-RAY DIFFRACTION94
3.0944-3.33320.28061580.216812233X-RAY DIFFRACTION99
3.3332-3.66850.25341590.191312302X-RAY DIFFRACTION100
3.6685-4.1990.20571610.163512276X-RAY DIFFRACTION99
4.199-5.2890.18971560.143312196X-RAY DIFFRACTION98
5.289-45.41060.20951530.161712039X-RAY DIFFRACTION96

+
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