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- PDB-2ftp: Crystal Structure of hydroxymethylglutaryl-CoA lyase from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2ftp
TitleCrystal Structure of hydroxymethylglutaryl-CoA lyase from Pseudomonas aeruginosa
Componentshydroxymethylglutaryl-CoA lyase
KeywordsLYASE / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3-hydroxy-3-isohexenylglutaryl-CoA lyase / 3-hydroxy-3-isohexenylglutaryl-CoA lyase activity / terpene catabolic process / hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / isoprenoid catabolic process / L-leucine catabolic process / metal ion binding
Similarity search - Function
Hydroxymethylglutaryl-CoA lyase, active site / Hydroxymethylglutaryl-coenzyme A lyase active site. / 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
: / 3-hydroxy-3-isohexenylglutaryl-CoA/hydroxy-methylglutaryl-CoA lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXiao, T. / Evdokimova, E. / Liu, Y. / Kudritska, M. / Savchenko, A. / Pai, E.F. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of hydroxymethylglutaryl-CoA lyase from Pseudomonas aeruginosa
Authors: Xiao, T. / Evdokimova, E. / Liu, Y. / Kudritska, M. / Savchenko, A. / Pai, E.F. / Edwards, A.
History
DepositionJan 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2754
Polymers32,0671
Non-polymers2073
Water3,999222
1
A: hydroxymethylglutaryl-CoA lyase
hetero molecules

A: hydroxymethylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5498
Polymers64,1352
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_544z+1/2,-y-1/2,x-1/21
Buried area3960 Å2
ΔGint-42 kcal/mol
Surface area22960 Å2
MethodPISA, PQS
2
A: hydroxymethylglutaryl-CoA lyase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)193,64824
Polymers192,4056
Non-polymers1,24318
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation37_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation43_544-x+1/2,-z-1/2,-y-1/21
crystal symmetry operation46_544z+1/2,-y-1/2,x-1/21
Buried area20020 Å2
ΔGint-125 kcal/mol
Surface area60750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.012, 189.012, 189.012
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein hydroxymethylglutaryl-CoA lyase


Mass: 32067.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 9948014, UniProt: Q9I2A0*PLUS, hydroxymethylglutaryl-CoA lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 4.41 Å3/Da / Density % sol: 72.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris 8.0, 3.4M Sodium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 11, 2005 / Details: xenocs multilayer confocal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→80 Å / Num. all: 22088 / Num. obs: 21999 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 42.6 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 42.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 9.97 / Num. unique all: 1126 / Rsym value: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDN

1ydn


Resolution: 2.4→80 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.446 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21309 735 3.2 %RANDOM
Rwork0.18713 ---
all0.18799 22088 --
obs0.18799 21999 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.229 Å2
Refinement stepCycle: LAST / Resolution: 2.4→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 13 222 2473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222326
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.973154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3175307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10923.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50715378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4881520
X-RAY DIFFRACTIONr_chiral_restr0.1260.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021782
X-RAY DIFFRACTIONr_nbd_refined0.2060.21198
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2175
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.229
X-RAY DIFFRACTIONr_mcbond_it0.611.51506
X-RAY DIFFRACTIONr_mcangle_it1.20222400
X-RAY DIFFRACTIONr_scbond_it2.1393839
X-RAY DIFFRACTIONr_scangle_it3.5814.5754
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 47 -
Rwork0.24 1584 -
obs--99.82 %

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