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- PDB-2x76: The crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolutio... -

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Basic information

Entry
Database: PDB / ID: 2x76
TitleThe crystal structure of PhaZ7 at atomic (1.2 Angstrom) resolution reveals details of the active site and suggests a substrate binding mode
ComponentsPHB DEPOLYMERASE PHAZ7
KeywordsHYDROLASE / BIOPOLYMERS / OXYANION HOLE / BIODEGRADATION / CATALYTIC TRIAD
Function / homology
Function and homology information


lipase activity / lipid catabolic process
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Lipase (Class 2)
Similarity search - Component
Biological speciesPAUCIMONAS LEMOIGNEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.45 Å
AuthorsWakadkar, S. / Hermawan, S. / Jendrossek, D. / Papageorgiou, A.C.
CitationJournal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2010
Title: The structure of PhaZ7 at atomic (1.2 A) resolution reveals details of the active site and suggests a substrate-binding mode.
Authors: Wakadkar, S. / Hermawan, S. / Jendrossek, D. / Papageorgiou, A.C.
History
DepositionFeb 24, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_symmetry / _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: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,60318
Polymers36,2371
Non-polymers1,36617
Water8,431468
1
A: PHB DEPOLYMERASE PHAZ7
hetero molecules

A: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,20636
Polymers72,4742
Non-polymers2,73234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4210 Å2
ΔGint-79.9 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.630, 140.580, 56.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2333-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHB DEPOLYMERASE PHAZ7 / PHAZ7


Mass: 36237.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 39-380 / Source method: isolated from a natural source / Source: (natural) PAUCIMONAS LEMOIGNEI (bacteria) / References: UniProt: Q939Q9

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Non-polymers , 5 types, 485 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.75 Å3/Da / Density % sol: 55.24 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PHAZ7 WAS CRYSTALLIZED USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 16 C. THE WELL SOLUTION CONSISTED OF 20% W/V PEG3350 AND 0.2 M NA IODIDE. A 1.5 MICROLITRES PROTEIN SOLUTION WAS MIXED ...Details: PHAZ7 WAS CRYSTALLIZED USING THE HANGING DROP VAPOR DIFFUSION METHOD AT 16 C. THE WELL SOLUTION CONSISTED OF 20% W/V PEG3350 AND 0.2 M NA IODIDE. A 1.5 MICROLITRES PROTEIN SOLUTION WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION ON SILICONIZED COVERSLIPS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. obs: 71446 / % possible obs: 99.9 % / Observed criterion σ(I): 3.9 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.1
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5.95 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: PDB ENTRY 2X5X

2x5x


Resolution: 1.45→20 Å / Num. parameters: 27833 / Num. restraintsaints: 34199 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.178 -5 %RANDOM
all0.1345 67830 --
obs--94.4 %-
Refine analyzeNum. disordered residues: 14 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3040.5
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 22 468 3039
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.497
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.083

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