[English] 日本語
Yorodumi
- PDB-4rvo: Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rvo
TitleCrystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution
ComponentsPhenylacetate-coenzyme A ligase
KeywordsLIGASE / Acetyl-CoA synthetase-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phenylacetate-CoA ligase / phenylacetate-CoA ligase activity / phenylacetate catabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Phenylacetate-CoA ligase / AMP-dependent ligase, C-terminal / AMP-binding enzyme C-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme ...Phenylacetate-CoA ligase / AMP-dependent ligase, C-terminal / AMP-binding enzyme C-terminal domain / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Unknown ligand / Phenylacetate-coenzyme A ligase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.41 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
SupersessionMar 18, 2015ID: 4R1W
Revision 1.1Mar 18, 2015Group: Advisory
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phenylacetate-coenzyme A ligase
B: Phenylacetate-coenzyme A ligase
C: Phenylacetate-coenzyme A ligase
D: Phenylacetate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,26948
Polymers200,8164
Non-polymers4,45344
Water9,782543
1
A: Phenylacetate-coenzyme A ligase
B: Phenylacetate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04428
Polymers100,4082
Non-polymers2,63626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-50 kcal/mol
Surface area34480 Å2
MethodPISA
2
C: Phenylacetate-coenzyme A ligase
D: Phenylacetate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,22520
Polymers100,4082
Non-polymers1,81718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-56 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.237, 210.223, 71.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Phenylacetate-coenzyme A ligase


Mass: 50203.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0428 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AAN6

-
Non-polymers , 10 types, 587 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE CONSTRUCT (RESIDUES 1-435) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-435) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.200M potassium sulfate, 20.00% polyethylene glycol 3350, No Buffer pH 6.7, 3mM D-fructose, 3mM CoA, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979251
ReflectionResolution: 2.41→46.574 Å / Num. all: 74114 / Num. obs: 74114 / % possible obs: 99 % / Redundancy: 3.5 % / Rsym value: 0.067 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.41-2.543.20.431.533580105920.4398.1
2.54-2.693.30.3162.333532100930.31698.8
2.69-2.883.40.2212.83245595370.22199.2
2.88-3.113.40.1774.33011588480.17798.1
3.11-3.413.60.10472954982220.10499.4
3.41-3.813.60.063122723874780.06399.7
3.81-4.43.60.039182406966700.03999.5
4.4-5.393.60.03222.12057056750.03299.7
5.39-7.623.60.02825.51606444510.02899.7
7.62-46.5743.40.01735.5878825480.01798.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.41→46.574 Å / Cor.coef. Fo:Fc: 0.9425 / Cor.coef. Fo:Fc free: 0.9243 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.PROTEIN ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION. 4. POTASSIUM (K) AND SULFATE (SO4) FROM THE CRYSTALLIZATION, AND ETHYLENE GLYCOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. POLYETHYLENE GLYCOL FRAGMENTS (PEG,PG4,AND PGE FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 6.ADENOSINE-5'-DIPHOSPHATE WAS MODELED INTO THE ACTIVE SITE ON THE FOUR SUBUNITS. UN-EXPLAINED ELECTRON DENSITIES ADJACENT TO THE ADP WERE MODELED AS UNKNOWN LIGANDS (UNL).7. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 8. TLS GROUPS WERE ASSIGNED WITH WITH THE AID OF THE TLS MOTION SERVER. 9.WATERS AND LIGANDS WERE EXCLUDED FROM TLS REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3726 5.03 %RANDOM
Rwork0.1874 ---
obs0.1888 74051 98.81 %-
Displacement parametersBiso max: 153.21 Å2 / Biso mean: 56.9627 Å2 / Biso min: 12.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.8042 Å20 Å20 Å2
2--3.9302 Å20 Å2
3---1.874 Å2
Refine analyzeLuzzati coordinate error obs: 0.364 Å
Refinement stepCycle: LAST / Resolution: 2.41→46.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13471 0 293 543 14307
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6709SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes369HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2087HARMONIC5
X-RAY DIFFRACTIONt_it14067HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC10
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1878SEMIHARMONIC5
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_contact16531SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14067HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19022HARMONIC100.36
X-RAY DIFFRACTIONt_omega_torsion3.92
X-RAY DIFFRACTIONt_other_torsion2.13
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2306 275 5.13 %
Rwork0.2131 5087 -
all0.214 5362 -
obs--98.81 %
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)
10.77350.367-0.12331.7308-0.47861.78750.00080.120.0615-0.25250.06220.07090.1558-0.0232-0.06290.304-0.007-0.0049-0.18720.0191-0.231-0.33261.019827.015
20.5811-2.7277-0.4014.07230.02213.01150.01050.0621-0.03150.0084-0.0692-0.0625-0.030.02110.05870.20890.0369-0.0642-0.1930.0682-0.044326.959246.901128.8122
30.87820.6847-0.33652.3051-0.44421.66480.0798-0.09630.00080.4107-0.0630.09370.0052-0.0257-0.01690.304-0.01820.0046-0.282-0.0064-0.2905-4.311148.187458.9661
43.9376-2.86291.5453.04171.19380-0.0131-0.0399-0.1501-0.028-0.04680.05040.0060.0130.05990.24270.0712-0.0871-0.23890.1309-0.029419.02232.535566.2524
51.74810.1359-0.01880.94680.17281.86170.0217-0.5125-0.07640.2661-0.0394-0.09820.40670.04990.01760.304-0.00090.0047-0.1660.0293-0.294139.1509-11.135574.8551
60.6956-0.50190.36184.01191.48954.31080.0013-0.0740.11670.03420.0070.0484-0.05180.0295-0.00820.2521-0.02730.0123-0.2169-0.0533-0.082341.96119.481373.6287
71.78170.43650.43491.08750.10941.42850.01890.14330.1404-0.1488-0.03410.07320.17540.00080.01530.3040.01860.0345-0.25290.0174-0.209926.1839-7.417842.834
80.85271.38550.01037.1003-0.87341.21760.00280.02770.0408-0.0875-0.06910.1273-0.0016-0.00320.06630.17940.0474-0.086-0.28160.15190.070225.284521.89135.5771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 332
2X-RAY DIFFRACTION2A333 - 433
3X-RAY DIFFRACTION3B3 - 323
4X-RAY DIFFRACTION4B324 - 432
5X-RAY DIFFRACTION5C0 - 329
6X-RAY DIFFRACTION6C330 - 433
7X-RAY DIFFRACTION7D2 - 332
8X-RAY DIFFRACTION8D333 - 433

+
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