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- PDB-2f9i: Crystal Structure of the carboxyltransferase subunit of ACC from ... -

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Basic information

Entry
Database: PDB / ID: 2f9i
TitleCrystal Structure of the carboxyltransferase subunit of ACC from Staphylococcus aureus
Components
  • acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
  • acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
KeywordsTRANSFERASE / zinc ribbon / crotonase superfamily / spiral domain
Function / homology
Function and homology information


acetyl-CoA carboxytransferase / carboxyl- or carbamoyltransferase activity / acetyl-CoA carboxylase complex / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / fatty acid biosynthetic process / zinc ion binding / ATP binding
Similarity search - Function
Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, alpha subunit / Acetyl co-enzyme A carboxylase carboxyltransferase-like / Acetyl-coA carboxylase zinc finger domain / Acetyl-CoA carboxylase zinc finger domain / Acetyl-CoA carboxylase carboxyl transferase, beta subunit / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / : / Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha / Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBilder, P.W.
CitationJournal: Biochemistry / Year: 2006
Title: The structure of the carboxyltransferase component of acetyl-coA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme.
Authors: Bilder, P. / Lightle, S. / Bainbridge, G. / Ohren, J. / Finzel, B. / Sun, F. / Holley, S. / Al-Kassim, L. / Spessard, C. / Melnick, M. / Newcomer, M. / Waldrop, G.L.
History
DepositionDec 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
B: acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
C: acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha
D: acetyl-coenzyme A carboxylase carboxyl transferase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3346
Polymers137,2034
Non-polymers1312
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-91 kcal/mol
Surface area42210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.979, 50.859, 149.639
Angle α, β, γ (deg.)90.00, 113.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARG1AA34 - 30747 - 320
21ASPASPARGARG1CC34 - 30747 - 320
12ILEILEVALVAL2BB29 - 28329 - 283
22ILEILEVALVAL2DD29 - 28329 - 283

NCS ensembles :
ID
1
2
DetailsThe biological assembly is a tetramer in the asymmetric unit

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Components

#1: Protein acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha


Mass: 36684.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: K-12 / Gene: ACCA,ACCD / Plasmid: pDEST-T7-202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: GenBank: 49244968, UniProt: Q2FG38*PLUS
#2: Protein acetyl-coenzyme A carboxylase carboxyl transferase subunit beta


Mass: 31916.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pDEST-T7-202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: GenBank: 49242071, UniProt: Q5HF73*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG-400, 0.1M HEPES, pH 8.0, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorDate: May 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 3 % / Number: 90018 / Rmerge(I) obs: 0.06 / Χ2: 1.077 / D res high: 1.98 Å / D res low: 50 Å / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.265097.910.0661.0623
3.394.2699.610.0411.0123.1
2.963.3999.610.0391.0813.1
2.692.9699.610.0521.0533.1
2.492.6999.810.0711.0953.1
2.352.4999.910.0951.1233.1
2.232.3599.910.1271.1163.1
2.132.2399.210.1751.0973
2.052.1394.910.2241.062.9
1.982.0582.310.2931.0722.7
ReflectionResolution: 1.98→50 Å / Num. obs: 90018 / % possible obs: 97.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.06 / Χ2: 1.077
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.293 / Num. unique all: 7562 / Χ2: 1.072 / % possible all: 82.3

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.15 / Packing: 0.357
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å15 Ågeneral98.4 0
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 90017
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
10.74-10040.50.161565
7.6-10.7436.90.7511045
6.2-7.638.70.7521415
5.37-6.244.10.7421665
4.8-5.3737.50.7871868
4.39-4.835.90.8032052
4.06-4.3937.80.8022228
3.8-4.0640.60.8052377
3.58-3.839.40.7962549
3.4-3.5840.90.7962650
3.24-3.441.20.7912847
3.1-3.2442.60.7792940
2.98-3.142.60.7583034
2.87-2.9842.40.7693213
2.77-2.8743.60.7673285
2.69-2.7745.10.753381
2.61-2.69440.7573530
2.53-2.6143.90.7483572
2.46-2.5344.90.7443764
2.4-2.4643.10.7493770
2.34-2.4440.7463931
2.29-2.3443.90.7463995
2.24-2.29450.7434108
2.19-2.2444.70.7544158
2.15-2.1945.20.7494230
2.11-2.1546.20.7494200
2.07-2.1146.20.744244
2.03-2.0749.10.734142
1.98-2.0353.90.6935259

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DM4.2phasing
DENZOdata reduction
PDB_EXTRACT1.701data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ON3

1on3


Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.434 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 9030 10 %RANDOM
Rwork0.186 ---
all0.189 ---
obs0.189 90017 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.884 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 2 583 9270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0228639
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.96911570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88451110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84824.176364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.653151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6191555
X-RAY DIFFRACTIONr_chiral_restr0.1030.21285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026408
X-RAY DIFFRACTIONr_nbd_refined0.2330.24456
X-RAY DIFFRACTIONr_nbtor_refined0.3080.26012
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2624
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3780.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.29
X-RAY DIFFRACTIONr_mcbond_it1.3321.55689
X-RAY DIFFRACTIONr_mcangle_it1.56228763
X-RAY DIFFRACTIONr_scbond_it2.59533312
X-RAY DIFFRACTIONr_scangle_it3.8354.52807
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2075TIGHT POSITIONAL0.20.05
1A2075TIGHT THERMAL1.180.5
2B1019TIGHT POSITIONAL0.120.05
2B919MEDIUM POSITIONAL0.340.5
2B1019TIGHT THERMAL1.220.5
2B919MEDIUM THERMAL1.572
LS refinement shellResolution: 1.982→2.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 558 -
Rwork0.253 5073 -
obs-5631 82.64 %

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