[English] 日本語
Yorodumi
- PDB-6n0z: Crystal structure of Anaerolinea thermophila mevalonate 5-phospha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n0z
TitleCrystal structure of Anaerolinea thermophila mevalonate 5-phosphate decarboxylase N20K H194M mutant complexed with (R)-MVAPP
ComponentsDiphosphomevalonate decarboxylase
KeywordsLYASE
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DP6 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesAnaerolinea thermophila
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNoel, J.P. / Thomas, S.T. / Louie, G.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase.
Authors: Thomas, S.T. / Louie, G.V. / Lubin, J.W. / Lundblad, V. / Noel, J.P.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Diphosphomevalonate decarboxylase
B: Diphosphomevalonate decarboxylase
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
E: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,36512
Polymers214,5176
Non-polymers1,8496
Water31,5981754
1
A: Diphosphomevalonate decarboxylase
E: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-33 kcal/mol
Surface area24840 Å2
MethodPISA
2
B: Diphosphomevalonate decarboxylase
F: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-31 kcal/mol
Surface area25510 Å2
MethodPISA
3
C: Diphosphomevalonate decarboxylase
D: Diphosphomevalonate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1224
Polymers71,5062
Non-polymers6162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-34 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.800, 138.090, 105.130
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Diphosphomevalonate decarboxylase /


Mass: 35752.770 Da / Num. of mol.: 6 / Mutation: D20K, H194M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerolinea thermophila (strain DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1) (bacteria)
Strain: DSM 14523 / JCM 11388 / NBRC 100420 / UNI-1 / Gene: mvaD, ANT_19910 / Production host: Escherichia coli (E. coli)
References: UniProt: E8N6F3, diphosphomevalonate decarboxylase
#2: Chemical
ChemComp-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O10P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1754 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M acetic acid pH 4.5 3-5% PEG 20,000 0.3 M ammonium acetate 5 mM (R)-MVAPP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.03 Å / Num. obs: 131416 / % possible obs: 79 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.624 / Num. unique obs: 10659 / % possible all: 65.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLM7.1.1data reduction
Aimless0.3.11data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HK2

2hk2


Resolution: 1.95→45.567 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.5
RfactorNum. reflection% reflection
Rfree0.2023 6583 5.01 %
Rwork0.1674 --
obs0.1691 131340 78.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→45.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14847 0 108 1754 16709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715287
X-RAY DIFFRACTIONf_angle_d0.86520824
X-RAY DIFFRACTIONf_dihedral_angle_d17.8755576
X-RAY DIFFRACTIONf_chiral_restr0.0522390
X-RAY DIFFRACTIONf_plane_restr0.0072665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.32071680.2613457X-RAY DIFFRACTION65
1.9722-1.99540.30642060.24743430X-RAY DIFFRACTION65
1.9954-2.01970.26931810.24473429X-RAY DIFFRACTION65
2.0197-2.04530.30941940.22823358X-RAY DIFFRACTION65
2.0453-2.07220.26611700.21413422X-RAY DIFFRACTION65
2.0722-2.10060.25121820.21323380X-RAY DIFFRACTION65
2.1006-2.13060.28291750.19923373X-RAY DIFFRACTION64
2.1306-2.16240.23091670.19943379X-RAY DIFFRACTION64
2.1624-2.19620.25241880.1963388X-RAY DIFFRACTION65
2.1962-2.23220.22841910.18213302X-RAY DIFFRACTION63
2.2322-2.27070.21921700.193330X-RAY DIFFRACTION64
2.2707-2.3120.24251810.18743350X-RAY DIFFRACTION63
2.312-2.35640.21791650.18593416X-RAY DIFFRACTION65
2.3564-2.40450.22892370.19034020X-RAY DIFFRACTION77
2.4045-2.45680.22861870.18744059X-RAY DIFFRACTION76
2.4568-2.51390.2392050.18584036X-RAY DIFFRACTION76
2.5139-2.57680.22742160.18773957X-RAY DIFFRACTION76
2.5768-2.64650.23341890.17693970X-RAY DIFFRACTION75
2.6465-2.72430.2172400.17373904X-RAY DIFFRACTION75
2.7243-2.81230.21371950.17044104X-RAY DIFFRACTION77
2.8123-2.91280.19372640.18055057X-RAY DIFFRACTION96
2.9128-3.02940.21972690.17645253X-RAY DIFFRACTION100
3.0294-3.16720.20573090.1665245X-RAY DIFFRACTION100
3.1672-3.33410.20052870.16655283X-RAY DIFFRACTION100
3.3341-3.5430.16492540.16055308X-RAY DIFFRACTION100
3.543-3.81640.18222830.14985264X-RAY DIFFRACTION100
3.8164-4.20020.17692770.13285301X-RAY DIFFRACTION100
4.2002-4.80740.1532580.12025334X-RAY DIFFRACTION100
4.8074-6.05460.17552900.15125277X-RAY DIFFRACTION100
6.0546-45.57970.15232850.14865371X-RAY DIFFRACTION100

+
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