[English] 日本語
Yorodumi
- PDB-3hyk: 2.31 Angstrom resolution crystal structure of a holo-(acyl-carrie... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hyk
Title2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from Bacillus anthracis str. Ames in complex with CoA (3',5'-ADP)
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / Holo-(Acyl-Carrier-Protein) Synthase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Fatty acid biosynthesis / Lipid synthesis / Magnesium / Metal-binding / CSGID
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
: / 4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHalavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria.
Authors: Halavaty, A.S. / Kim, Y. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Kwon, K. / Peterson, S.N. / Joachimiak, A. / ...Authors: Halavaty, A.S. / Kim, Y. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Kwon, K. / Peterson, S.N. / Joachimiak, A. / Savchenko, A. / Anderson, W.F.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Dec 5, 2012Group: Database references
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holo-[acyl-carrier-protein] synthase
B: Holo-[acyl-carrier-protein] synthase
C: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,59424
Polymers40,5993
Non-polymers2,99521
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-191 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.526, 77.526, 122.965
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase acpS


Mass: 13533.095 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Bacillus anthracis str. Ames / Gene: acpS, BA_0250, GBAA_0250, BAS0236 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)
References: UniProt: Q81JG3, holo-[acyl-carrier-protein] synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein was mixed at 1:1 v/v ratio with PEG3350 25%, 0.2M MgCl2, 0.1M Hepes pH 7.5, 10mM CoA. 5% Glycerol, 5% sucrose, 55 Eth. Gl. in magic sol., paratone were used as cryo protectants. , ...Details: protein was mixed at 1:1 v/v ratio with PEG3350 25%, 0.2M MgCl2, 0.1M Hepes pH 7.5, 10mM CoA. 5% Glycerol, 5% sucrose, 55 Eth. Gl. in magic sol., paratone were used as cryo protectants. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2009 / Details: beryllium lenses
RadiationMonochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.31→34.99 Å / Num. all: 19381 / Num. obs: 19381 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.54
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.9 / Num. unique all: 969 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F09

3f09
PDB Unreleased entry


Resolution: 2.31→34.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.325 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24654 986 5.1 %RANDOM
Rwork0.18962 ---
obs0.19263 18306 99.51 %-
all-18306 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.961 Å2
Baniso -1Baniso -2Baniso -3
1--2.56 Å2-1.28 Å20 Å2
2---2.56 Å20 Å2
3---3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.31→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 177 260 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223023
X-RAY DIFFRACTIONr_bond_other_d0.0010.022029
X-RAY DIFFRACTIONr_angle_refined_deg1.7442.0344106
X-RAY DIFFRACTIONr_angle_other_deg0.78434973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7045371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.03924.132121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11815563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9141522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8751.51799
X-RAY DIFFRACTIONr_mcbond_other0.2391.5747
X-RAY DIFFRACTIONr_mcangle_it1.60322917
X-RAY DIFFRACTIONr_scbond_it3.08531224
X-RAY DIFFRACTIONr_scangle_it4.7264.51189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.307→2.367 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 64 -
Rwork0.186 1299 -
obs--97.08 %
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)
13.67530.0742-0.49623.76310.42060.5621-0.0213-0.4456-0.02430.3060.0974-0.3196-0.02440.0921-0.0760.06980.0193-0.01770.08390.01230.048467.53857.67655.5215
22.5032-0.1958-0.38661.53130.5961.45460.0745-0.17680.29170.04970.0584-0.4508-0.19790.186-0.13290.0553-0.0048-0.01610.0685-0.0190.159972.972312.51632.5325
32.9152-0.2278-0.91613.99151.00612.16810.0820.23540.1272-0.2959-0.1219-0.1454-0.12670.04530.03990.02420.01270.01150.04670.02540.01864.32714.8564-4.7041
44.3319-0.8492-1.97354.4426-1.0372.5059-0.0031-0.19070.27890.57660.05690.1185-0.163-0.1027-0.05370.1221-0.0427-0.00080.1271-0.04930.091647.600518.46566.6881
51.91650.536-0.15122.9772-0.18011.0034-0.0213-0.00950.06270.01570.03970.382-0.0569-0.1818-0.01850.00970.02050.00140.05080.00340.049142.835815.19480.005
68.0297-4.1312-6.23882.25653.10324.94440.16450.23330.33-0.1742-0.1006-0.3383-0.0624-0.1761-0.06380.157-0.01570.02710.01110.03180.370351.587512.3889-11.8572
72.84590.29951.52374.5328-1.28572.73080.1562-0.361-0.20710.2899-0.22640.05010.21670.03980.07020.06720.00710.02850.14140.02030.0750.4779-4.71876.8084
83.3043-0.07870.31561.8015-0.47130.89320.01220.0239-0.3686-0.01260.0047-0.09410.20630.0674-0.01690.05510.0189-0.00280.0143-0.00290.047254.7226-8.11470.0589
92.3892-0.5737-1.00942.1610.2298.202-0.14070.3125-0.0547-0.3497-0.00470.24970.1246-0.23170.14540.092-0.0274-0.03720.07160.01220.036952.47150.2266-16.6677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 26
2X-RAY DIFFRACTION2A27 - 77
3X-RAY DIFFRACTION3A78 - 118
4X-RAY DIFFRACTION4B0 - 29
5X-RAY DIFFRACTION5B30 - 110
6X-RAY DIFFRACTION6B111 - 117
7X-RAY DIFFRACTION7C0 - 27
8X-RAY DIFFRACTION8C28 - 112
9X-RAY DIFFRACTION9C113 - 118

+
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