[English] 日本語
Yorodumi
- PDB-4r1l: Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r1l
TitleCrystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 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 / ADENOSINE MONOPHOSPHATE / COENZYME A / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phenylacetate-coenzyme A ligase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)206,49742
Polymers200,8164
Non-polymers5,68138
Water10,016556
1
A: Phenylacetate-coenzyme A ligase
B: Phenylacetate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,59423
Polymers100,4082
Non-polymers3,18621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-66 kcal/mol
Surface area33880 Å2
MethodPISA
2
C: Phenylacetate-coenzyme A ligase
D: Phenylacetate-coenzyme A ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,90319
Polymers100,4082
Non-polymers2,49517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-60 kcal/mol
Surface area34330 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20040 Å2
ΔGint-149 kcal/mol
Surface area66280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.701, 211.141, 71.861
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (bacteria)
Strain: VPI-5482 / Gene: BT_0428 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AAN6

-
Non-polymers , 10 types, 594 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


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.2M potassium sulfate, 20.0% polyethylene glycol 3350, No Buffer pH 6.7, 3mM phenylacetate, 3mM AMP, 3mM CoenzymeA, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 22, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 2.42→48.782 Å / Num. obs: 74457 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.446 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.41-2.50.4882.625959703790.6
2.5-2.60.4053.228044744099.7
2.6-2.710.313426366698499.7
2.71-2.860.2295.329700784999.7
2.86-3.030.196.526086706498.8
3.03-3.270.1189.629263774599.5
3.27-3.60.07214.528454755199.4
3.6-4.110.0519.927808739199
4.11-5.170.0424.528585760898.6
5.170.04226.628623778896.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→48.782 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9209 / 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. THE MODELING OF ZINC IS SUPPORTED BY X-RAY FLUORESCENCE AND ANOMALOUS DIFFERENCE MAPS. 5. POTASSIUM (K), SULFATE (SO4), AND POLYETHYLENE GLYCOL FRAGMENTS (PEG),(PGE) FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. 6. 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WAS MODELED INTO THE STRUCTURE. 6. ADENOSINE-5'-MONOSPHATE (AMP), A CRYSTALLIZATION ADDITIVE, WAS MODELED INTO THE ACTIVE SITE ON ALL FOUR SUBUNITS IN THE ASYMMETRIC UNIT. ADDITIONAL ELECTRON DENSITY AT THE ACTIVE SITE ON SUBUNITS A,B, AND D INDICATED A MIXTURE OF AMP AND ADENOSINE-5'-DIPHOSPHATE (ADP). THEREFORE, BOTH AMP AND ADP WERE MODELED EACH WITH A PARTIAL OCCUPANCY OF 0.5 INTO THE ACTIVE SITE ON THESE THREE SUBUNITS. SUBUNIT C DID NOT SHOW ADDITIONAL DENSITY FOR ADP AND WAS MODELED WITH AMP AT FULL OCCUPANCY. 7.COENZYME A, (COA), WAS MODELED WITH PARTIAL OCCUPANCY INTO INTO SUBUNITS A AND C. HOWEVER, ELECTRON DENSITY FOR THE PANTOTHENATIC ACID MOIETIES WERE DISORDERED AND THIS PORTION OF THE COA MOLECULE COULD NOT BE RELIABLY MODELED. 8. ASN 243 ON THE A,B,C, AND D-CHAINS ARE RAMACHANDRAN OUTLIERS IN MOLPROBITY EVEN THOUGH THEIR POSITIONING IS SUPPORTED BY ELECTRON DENSITY. ASP 384 ON THE C-CHAIN IS IN A REGION OF POOR ELECTRON DENSITY AND IS FLAGGED AS RAMACHANDRAN OUTLIER IN MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 3742 5.04 %RANDOM
Rwork0.1725 ---
obs0.1745 74242 99 %-
Displacement parametersBiso max: 155.79 Å2 / Biso mean: 54.7539 Å2 / Biso min: 13.04 Å2
Baniso -1Baniso -2Baniso -3
1--9.3255 Å20 Å20 Å2
2--7.2042 Å20 Å2
3---2.1213 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2.42→48.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13425 0 299 556 14280
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6737SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes376HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2129HARMONIC5
X-RAY DIFFRACTIONt_it14113HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1885SEMIHARMONIC5
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_contact16601SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14113HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19118HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion2.27
LS refinement shellResolution: 2.42→2.48 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 275 5.03 %
Rwork0.2006 5190 -
all0.2022 5465 -
obs--99 %
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)
10.93690.5389-0.28961.8844-1.09172.1029-0.04920.17770.1634-0.25160.15420.15280.1871-0.1566-0.105-0.0619-0.03120.007-0.08270.0566-0.1324-0.054161.046927.4074
25.2557-2.70770.04363.6503-0.07233.50380.05240.2063-0.05250.1516-0.2254-0.2735-0.01990.0290.1731-0.1764-0.01730.0287-0.12110.12650.057227.660946.443829.1941
31.11330.8206-0.29362.3606-0.91581.42270.1772-0.09930.08630.5442-0.07420.2079-0.1287-0.0826-0.10290.1381-0.05080.0775-0.1813-0.0028-0.2215-4.333148.412759.3175
48.2541-2.91042.06382.69470.3030.0023-0.0149-0.1922-0.4774-0.1187-0.13770.00730.0360.03610.1525-0.0517-0.0259-0.1508-0.29550.1520.208819.017233.030466.8326
51.870.65450.13121.30630.48262.06470.1516-0.516-0.1810.5044-0.0658-0.29790.54420.1274-0.08580.09960.0095-0.0825-0.14440.0235-0.256639.0338-11.115374.9648
62.78620.0066-0.32687.83570.99972.4307-0.0217-0.17620.35850.17610.09970.0419-0.17420.0766-0.078-0.067-0.0468-0.0562-0.1382-0.0872-0.070441.737519.401173.4217
72.09110.65210.49981.74960.19191.34490.02210.22810.0728-0.26290.02680.06340.1449-0.0116-0.0490.05360.01470.0064-0.1352-0.0029-0.182426.1119-7.602842.8661
81.46521.6727-0.69698.3154-1.0671.2844-0.01390.1460.4949-0.2678-0.25380.3019-0.0858-0.00950.2677-0.07740.0438-0.152-0.26480.1520.101525.69521.271735.1871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|0-338}
2X-RAY DIFFRACTION2{A|339-434}
3X-RAY DIFFRACTION3{B|4-325}
4X-RAY DIFFRACTION4{B|326-432}
5X-RAY DIFFRACTION5{C|0-330}
6X-RAY DIFFRACTION6{C|331-433}
7X-RAY DIFFRACTION7{D|2-332}
8X-RAY DIFFRACTION8{D|333-434}

+
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://pdbjlc1.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