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- PDB-1hux: CRYSTAL STRUCTURE OF THE ACIDAMINOCOCCUS FERMENTANS (R)-2-HYDROXY... -

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Basic information

Entry
Database: PDB / ID: 1hux
TitleCRYSTAL STRUCTURE OF THE ACIDAMINOCOCCUS FERMENTANS (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE COMPONENT A
ComponentsACTIVATOR OF (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE
KeywordsMETAL BINDING PROTEIN / actin fold
Function / homology
Function and homology information


glutamate catabolic process via 2-hydroxyglutarate / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / 4 iron, 4 sulfur cluster binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
CoA enzyme activase / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / (R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase
Similarity search - Component
Biological speciesAcidaminococcus fermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsLocher, K.P. / Hans, M. / Yeh, A.P. / Schmid, B. / Buckel, W. / Rees, D.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A.
Authors: Locher, K.P. / Hans, M. / Yeh, A.P. / Schmid, B. / Buckel, W. / Rees, D.C.
History
DepositionJan 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE TEN ADDITIONAL RESIDUES AT THE C-TERMINUS CORRESPOND TO AN ENGINEERED STREP-II TAG ...SEQUENCE THE TEN ADDITIONAL RESIDUES AT THE C-TERMINUS CORRESPOND TO AN ENGINEERED STREP-II TAG THAT APPEARS DISORDERED IN THE STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIVATOR OF (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE
B: ACTIVATOR OF (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2105
Polymers57,0032
Non-polymers1,2063
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-42 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.070, 51.990, 74.700
Angle α, β, γ (deg.)90.00, 118.81, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains the functional homodimer with the bridging [4Fe-4S] cluster

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Components

#1: Protein ACTIVATOR OF (R)-2-HYDROXYGLUTARYL-COA DEHYDRATASE


Mass: 28501.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus fermentans (bacteria) / Gene: HGDC / Plasmid: PMH6 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 BLUE / References: UniProt: P11568
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM sodium citrate pH 5.6, 20% PEG 4000, 20% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-40 mg/mlprotein1drop
250 mMTris-HCl1drop
30.3 M1dropNaCl
410 mM1dropMgCl2
51 mMADP1drop
6100 mMsodium citrate1reservoir
720 %(w/v)PEG40001reservoir
820 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.6920, 1.7395, 1.7419, 1.7968
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 1999
RadiationMonochromator: Double Crystal Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.6921
21.73951
31.74191
41.79681
ReflectionResolution: 3→43 Å / Num. all: 11525 / Num. obs: 11525 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 6.92 % / Biso Wilson estimate: 56.32 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 10 / Rsym value: 0.203 / % possible all: 100
Reflection
*PLUS
Num. measured all: 79725
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber (CNS)
RfactorNum. reflectionSelection details
Rfree0.279 2125 RANDOM
Rwork0.236 --
all-21674 -
obs-21635 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 62 0 3856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.326

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