[English] 日本語
Yorodumi
- PDB-7t71: Crystal Structure of Mevalonate 3,5-Bisphosphate Decarboxylase fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7t71
TitleCrystal Structure of Mevalonate 3,5-Bisphosphate Decarboxylase from Picrophilus Torridus
ComponentsMevalonate 3,5-bisphosphate decarboxylase
KeywordsLYASE / mevalonate pathway / mevalonic acid
Function / homology
Function and homology information


bisphosphomevalonate decarboxylase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / carboxy-lyase activity
Similarity search - Function
: / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / 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
OLEIC ACID / Mevalonate 3,5-bisphosphate decarboxylase
Similarity search - Component
Biological speciesPicrophilus torridus DSM 9790 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsVinokur, J.M. / Sawaya, M.R. / Cascio, D. / Collazo, M. / Bowie, J.U.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)DGE-1144087 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure of mevalonate 3,5-bisphosphate decarboxylase reveals insight into the evolution of decarboxylases in the mevalonate metabolic pathways.
Authors: Aoki, M. / Vinokur, J. / Motoyama, K. / Ishikawa, R. / Collazo, M. / Cascio, D. / Sawaya, M.R. / Ito, T. / Bowie, J.U. / Hemmi, H.
History
DepositionDec 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mevalonate 3,5-bisphosphate decarboxylase
B: Mevalonate 3,5-bisphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7723
Polymers84,4902
Non-polymers2821
Water2,054114
1
A: Mevalonate 3,5-bisphosphate decarboxylase
hetero molecules

B: Mevalonate 3,5-bisphosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)84,7723
Polymers84,4902
Non-polymers2821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x+1/2,y+1/2,-z+21
Buried area3070 Å2
ΔGint-16 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.560, 125.490, 52.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Mevalonate 3,5-bisphosphate decarboxylase / MBD / Bisphosphomevalonate decarboxylase


Mass: 42244.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picrophilus torridus DSM 9790 (archaea)
Strain: ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828 / Gene: PTO0478 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6L1T9, bisphosphomevalonate decarboxylase
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Final drop concentration: 1.4 M sodium malonate, 1.0 M NaCl, protein concentration 5.5 mg/ml

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.19→97.17 Å / Num. obs: 52437 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 10.838 % / Biso Wilson estimate: 41.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.117 / Χ2: 1.085 / Net I/σ(I): 15.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.19-2.259.6690.8762.9235460.8520.92492.4
2.25-2.3111.5850.7544.1437320.9210.789100
2.31-2.3811.5090.6424.9136780.9490.671100
2.38-2.4511.4730.5535.7535110.9620.579100
2.45-2.5311.4690.461734380.9740.483100
2.53-2.6211.2710.3937.8733640.9770.41199.9
2.62-2.7211.0310.3159.2932160.9860.331100
2.72-2.8310.0310.25310.5730790.9860.266100
2.83-2.9511.7010.21213.2329910.9920.22299.9
2.95-3.111.6890.16316.4128520.9950.17100
3.1-3.2711.3610.12120.6427290.9960.127100
3.27-3.4611.0460.123.6125860.9970.105100
3.46-3.710.5080.08326.5324310.9960.087100
3.7-49.7240.0728.5222780.9970.07499.8
4-4.389.3910.06430.6120980.9970.06899.8
4.38-4.910.4940.05934.6518990.9980.062100
4.9-5.6610.2270.05833.6817110.9980.06199.9
5.66-6.93100.05931.7614500.9980.062100
6.93-9.89.1080.04533.7611560.9990.04799.4
9.8-97.179.7270.04537.216920.9960.04799.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QT5

3qt5


Resolution: 2.19→97.17 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.171 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.148
RfactorNum. reflection% reflectionSelection details
Rfree0.207 5298 10.1 %RANDOM
Rwork0.184 ---
obs0.187 52436 99.3 %-
Displacement parametersBiso max: 124.64 Å2 / Biso mean: 42.46 Å2 / Biso min: 22.01 Å2
Baniso -1Baniso -2Baniso -3
1-5.4342 Å20 Å20 Å2
2--3.6172 Å20 Å2
3----9.0515 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.19→97.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5429 0 20 114 5563
Biso mean--54.48 43.79 -
Num. residues----695
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1893SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes835HARMONIC5
X-RAY DIFFRACTIONt_it5563HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion742SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6476SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5563HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7516HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion18.32
LS refinement shellResolution: 2.19→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2896 377 10.89 %
Rwork0.2628 3086 -
all0.2657 3463 -
obs--90.47 %
Refinement TLS params.Method: refined / Origin x: 38.3927 Å / Origin y: 27.738 Å / Origin z: 58.3124 Å
111213212223313233
T-0.0636 Å2-0.0039 Å2-0.0171 Å2--0.0227 Å2-0.0037 Å2---0.0262 Å2
L0.4615 °2-0.2512 °2-0.0647 °2-0.5237 °20.032 °2--0.1696 °2
S-0.0077 Å °-0.0347 Å °0.0123 Å °-0.0101 Å °0.0285 Å °-0.027 Å °-0.022 Å °0.0034 Å °-0.0208 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 349
2X-RAY DIFFRACTION1{ *|* }B1 - 349
3X-RAY DIFFRACTION1{ *|* }C1 - 349
4X-RAY DIFFRACTION1{ *|* }E1 - 349

+
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