[English] 日本語
Yorodumi
- PDB-6nds: Structure of an HMG-CoA lyase from Acenitobacter baumannii in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nds
TitleStructure of an HMG-CoA lyase from Acenitobacter baumannii in complex with coenzyme A and 3-methylmalate
Components3-hydroxy-3-methylglutaryl-CoA lyase
KeywordsLYASE / SSGCID / Acinetobacter baumannii / 3-hydroxy-3-methylglutaryl-CoA / CoA / beta-methylmalate / HMG / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / L-leucine catabolic process / metal ion binding
Similarity search - Function
HMG-CoA lyase / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / COENZYME A / 3-hydroxy-3-methylglutaryl-CoA lyase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of an HMG-CoA lyase from Acenitobacter baumannii in complex with coenzyme A and 3-methylmalate
Authors: Mayclin, S.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0838
Polymers34,8191
Non-polymers1,2647
Water4,810267
1
A: 3-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules

A: 3-hydroxy-3-methylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,16616
Polymers69,6372
Non-polymers2,52914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7540 Å2
ΔGint-85 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.460, 91.460, 78.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein 3-hydroxy-3-methylglutaryl-CoA lyase / Hydroxymethylglutaryl-CoA lyase / Hydroxymethylglutaryl-CoA lyase YngG


Mass: 34818.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: yngG_1, ABUW_2506, CBI29_01513, DV997_16665 / Plasmid: AcbaC.18886.a.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D5YK08, hydroxymethylglutaryl-CoA lyase

-
Non-polymers , 6 types, 274 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Top96 D11 (298571d11): 2 0.1 M Sodium Acetate: HCl, pH 4.6, 8% (w/v) PEG4000, 4mM NAD (bsi1606), 4mM HMG-CoA (bsi108595); AcbaC.18179.a.B1.PW38191 conc 23.33mg/mL; 20eg; puck/pin ID tud0-16

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.73 Å / Num. obs: 40790 / % possible obs: 100 % / Redundancy: 8.605 % / Biso Wilson estimate: 31.195 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.061 / Χ2: 1.003 / Net I/σ(I): 20.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.696.240.5622.9129600.8520.61399.7
1.69-1.748.0180.4914.1528860.9190.525100
1.74-1.799.1840.3725.8528250.9680.395100
1.79-1.849.1450.2667.8827380.9820.281100
1.84-1.918.9710.19610.2326680.9880.208100
1.91-1.978.6160.15512.6425650.9920.165100
1.97-2.058.9430.11516.1924870.9950.122100
2.05-2.139.1690.10119.0324050.9960.107100
2.13-2.229.0940.08122.6723000.9970.086100
2.22-2.338.5220.07125.2921990.9970.07599.9
2.33-2.468.7390.06427.4721150.9980.068100
2.46-2.619.20.05831.0419910.9980.06299.9
2.61-2.799.0470.05433.6318680.9980.057100
2.79-3.018.5440.0535.5217690.9980.05499.9
3.01-3.38.6550.04738.8616340.9980.05100
3.3-3.698.9780.04442.2214800.9990.04799.9
3.69-4.268.4840.04243.0913150.9990.04599.9
4.26-5.228.3040.04343.311460.9980.046100
5.22-7.388.3230.04541.998970.9990.048100
7.38-507.4630.04142.075420.9980.04499.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
Cootmodel building
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→45.73 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1677 2379 6.03 %
Rwork0.1532 37070 -
obs0.1541 39449 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.78 Å2 / Biso mean: 29.1193 Å2 / Biso min: 13.4 Å2
Refinement stepCycle: final / Resolution: 1.65→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 75 268 2620
Biso mean--44.23 38.78 -
Num. residues----305
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6499-1.68360.30941210.2398192387
1.6836-1.72020.22161370.2106200991
1.7202-1.76020.21861410.1782202292
1.7602-1.80430.17761170.1618210694
1.8043-1.85310.18751550.1542208195
1.8531-1.90760.1471200.1503215196
1.9076-1.96920.18771460.1601215697
1.9692-2.03950.19951390.149217398
2.0395-2.12120.17161410.1526221598
2.1212-2.21770.1411360.1426222499
2.2177-2.33460.18351380.1397221798
2.3346-2.48090.18071500.1497222399
2.4809-2.67240.16421430.15212252100
2.6724-2.94130.18451350.15432279100
2.9413-3.36680.16471490.15442284100
3.3668-4.24140.15421490.13952306100
4.2414-500.14691620.15922449100
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)
13.3207-1.64351.73253.1558-0.99992.62990.01180.0921-0.0416-0.09810.03570.0945-0.01610.048-0.04670.1201-0.02440.02630.1110.00130.1177-11.425931.69064.3439
21.04630.97480.15683.370.11651.7179-0.09430.24120.0935-0.36050.07040.04690.02110.0509-0.00850.1988-0.01430.01250.21670.00140.1478-10.552127.6572-6.3483
30.94190.35890.1941.424-0.36151.8767-0.05810.265-0.142-0.35850.0805-0.11770.29120.0037-0.00850.23930.01520.03220.203-0.05260.18-10.099312.8009-2.1001
41.9177-0.3522-0.39992.6005-0.05061.690.0147-0.05170.09190.1175-0.02240.1303-0.0654-0.12390.00160.11890.0016-0.00380.1452-0.00680.1432-11.360325.135817.2768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 62 )A1 - 62
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 117 )A63 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 214 )A118 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 305 )A215 - 305

+
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