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- PDB-3gf7: Glutaconyl-coA decarboxylase A subunit from Clostridium symbiosum... -

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Basic information

Entry
Database: PDB / ID: 3gf7
TitleGlutaconyl-coA decarboxylase A subunit from Clostridium symbiosum apoprotein
ComponentsGlutaconyl-CoA decarboxylase subunit A
KeywordsLYASE / glutaconyl-CoA decarboxylase / sodium ion transport / biotin / glutamate fermentation
Function / homology
Function and homology information


Single Helix bin / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / 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 ...Single Helix bin / Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaconyl-CoA decarboxylase subunit A
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKress, D. / Brugel, D. / Buckel, W. / Essen, L.-O.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases
Authors: Kress, D. / Brugel, D. / Schall, I. / Linder, D. / Buckel, W. / Essen, L.-O.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Glutaconyl-CoA decarboxylase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1202
Polymers65,0241
Non-polymers961
Water3,621201
1
A: Glutaconyl-CoA decarboxylase subunit A
hetero molecules

A: Glutaconyl-CoA decarboxylase subunit A
hetero molecules

A: Glutaconyl-CoA decarboxylase subunit A
hetero molecules

A: Glutaconyl-CoA decarboxylase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,4808
Polymers260,0964
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area27660 Å2
ΔGint-173 kcal/mol
Surface area64470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.050, 143.530, 167.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Glutaconyl-CoA decarboxylase subunit A


Mass: 65023.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Strain: HB25 / Gene: gcdA / Plasmid: pASK-IBA7plus / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: B7TVP1, EC: 4.1.1.70
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.36 Å3/Da / Density % sol: 47.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 2.4→32.987 Å / Num. obs: 24154 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 9.07
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.536.20.3342.32154534770.334100
2.53-2.686.20.2622.92055833230.262100
2.68-2.876.20.1941927531150.19100
2.87-3.16.20.1216.21791028950.121100
3.1-3.396.20.0789.51657226920.078100
3.39-3.796.20.05313.31495124250.053100
3.79-4.386.10.0416.41320421480.04100
4.38-5.376.10.03815.91118418300.03899.9
5.37-7.5960.0415.2871514440.0499.8
7.59-34.225.70.03812.945698050.03898.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PIX

1pix


Resolution: 2.4→32.48 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.86 / SU B: 6.585 / SU ML: 0.159 / SU R Cruickshank DPI: 0.403 / SU Rfree: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1002 4.1 %RANDOM
Rwork0.185 ---
obs0.187 24153 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 74.24 Å2 / Biso mean: 31.586 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å20 Å2
2--0.55 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 5 201 4408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224300
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9725831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97225.078193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4661519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023300
X-RAY DIFFRACTIONr_nbd_refined0.1990.22458
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22991
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2360
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.2198
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.240
X-RAY DIFFRACTIONr_mcbond_it0.4811.52766
X-RAY DIFFRACTIONr_mcangle_it0.83124347
X-RAY DIFFRACTIONr_scbond_it0.98831745
X-RAY DIFFRACTIONr_scangle_it1.5854.51484
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 81 -
Rwork0.2 1682 -
all-1763 -
obs--100 %

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