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- PDB-3d0k: Crystal structure of the LpqC, poly(3-hydroxybutyrate) depolymera... -

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Basic information

Entry
Database: PDB / ID: 3d0k
TitleCrystal structure of the LpqC, poly(3-hydroxybutyrate) depolymerase from Bordetella parapertussis
ComponentsPutative poly(3-hydroxybutyrate) depolymerase LpqC
KeywordsHYDROLASE / alpha-beta-alpha sandwich / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Alpha/beta hydrolase
Function and homology information
Biological speciesBordetella parapertussis 12822 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the LpqC, Poly(3-hydroxybutyrate) Depolymerase from Bordetella parapertussis.
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionMay 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Putative poly(3-hydroxybutyrate) depolymerase LpqC
B: Putative poly(3-hydroxybutyrate) depolymerase LpqC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,72120
Polymers67,3242
Non-polymers1,39718
Water7,909439
1
A: Putative poly(3-hydroxybutyrate) depolymerase LpqC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,35510
Polymers33,6621
Non-polymers6939
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative poly(3-hydroxybutyrate) depolymerase LpqC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,36610
Polymers33,6621
Non-polymers7049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.879, 83.710, 90.792
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

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Components

#1: Protein Putative poly(3-hydroxybutyrate) depolymerase LpqC


Mass: 33661.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-term maltose binding protein fusion-6-His-tag with TVMV protease and TEV protease cut sites
Source: (gene. exp.) Bordetella parapertussis 12822 (bacteria)
Strain: 12822 / NCTC 13253 / Gene: BPP4128 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7W3B7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% Dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2008 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→41.83 Å / Num. all: 54978 / Num. obs: 54978 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 20.67 Å2 / Rsym value: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 2697 / Rsym value: 0.598 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.83→41.83 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.264 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2803 5.1 %RANDOM
Rwork0.164 ---
all0.166 52230 --
obs0.166 52230 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-0.37 Å2
2--1.35 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.83→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 72 439 5041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.9446643
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63422.36250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5181552
X-RAY DIFFRACTIONr_chiral_restr0.1190.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023920
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22397
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23262
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2416
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0771.53035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70524738
X-RAY DIFFRACTIONr_scbond_it3.07532074
X-RAY DIFFRACTIONr_scangle_it4.7044.51905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 214 -
Rwork0.221 3773 -
obs-3987 99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57060.10830.3970.63830.39521.29580.0075-0.0272-0.00490.017-0.0198-0.0233-0.0016-0.07020.0123-0.05990.0137-0.01-0.0403-0.023-0.028919.743330.143292.8531
20.5549-0.06420.26260.5327-0.19360.9334-0.0238-0.004-0.0163-0.02690.0276-0.03070.00140.0066-0.0038-0.0404-0.00740.011-0.0551-0.0092-0.028613.323133.935342.2585
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2968 - 299
2X-RAY DIFFRACTION2BB2 - 2965 - 299

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