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- PDB-1ydn: Crystal Structure of the HMG-CoA Lyase from Brucella melitensis, ... -

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Basic information

Entry
Database: PDB / ID: 1ydn
TitleCrystal Structure of the HMG-CoA Lyase from Brucella melitensis, Northeast Structural Genomics Target LR35.
ComponentsHYDROXYMETHYLGLUTARYL-COA LYASE
KeywordsLYASE / TIM-barrel protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / L-leucine catabolic process / metal ion binding
Similarity search - Function
HMG-CoA lyase / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Hydroxymethylglutaryl-CoA lyase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsForouhar, F. / Abashidze, M. / Hussain, M. / Vorobiev, S.M. / Xiao, R. / Ciano, M. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds.
Authors: Forouhar, F. / Hussain, M. / Farid, R. / Benach, J. / Abashidze, M. / Edstrom, W.C. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Fu, Z. / Kim, J.J. / Miziorko, H.M. / Montelione, G.T. / Hunt, J.F.
History
DepositionDec 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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.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.conn_type_id / _struct_conn.id / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYMETHYLGLUTARYL-COA LYASE
B: HYDROXYMETHYLGLUTARYL-COA LYASE
C: HYDROXYMETHYLGLUTARYL-COA LYASE
D: HYDROXYMETHYLGLUTARYL-COA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,7128
Polymers126,5524
Non-polymers1604
Water10,737596
1
A: HYDROXYMETHYLGLUTARYL-COA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6782
Polymers31,6381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYDROXYMETHYLGLUTARYL-COA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6782
Polymers31,6381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HYDROXYMETHYLGLUTARYL-COA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6782
Polymers31,6381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HYDROXYMETHYLGLUTARYL-COA LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6782
Polymers31,6381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.272, 86.399, 87.683
Angle α, β, γ (deg.)90.00, 118.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HYDROXYMETHYLGLUTARYL-COA LYASE


Mass: 31637.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / Gene: GeneID:1197637 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q8YEF2, hydroxymethylglutaryl-CoA lyase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 200 mM CaCl2, and 10 mM DTT., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9878 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 12, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9878 Å / Relative weight: 1
ReflectionResolution: 2.3→28.94 Å / Num. all: 98524 / Num. obs: 97811 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.97 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.099 / Net I/σ(I): 13.91
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 0.219 / Num. unique all: 9816 / Rsym value: 0.0556 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→28.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 272181.43 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 8764 9.9 %RANDOM
Rwork0.271 ---
all0.275 97811 --
obs0.271 88898 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.8118 Å2 / ksol: 0.293899 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-9.2 Å20 Å24.55 Å2
2---12.64 Å20 Å2
3---3.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8372 0 4 596 8972
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.346 1353 10.1 %
Rwork0.296 11990 -
obs-8764 85.2 %

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