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- PDB-4bvl: Structure of 202-208 deletion mutant of PhaZ7 PHB depolymerase -

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Basic information

Entry
Database: PDB / ID: 4bvl
TitleStructure of 202-208 deletion mutant of PhaZ7 PHB depolymerase
ComponentsPHB DEPOLYMERASE PHAZ7
KeywordsHYDROLASE / CATALYTIC TRIAD / BIOPOLYMER BINDING
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
Biological speciesPAUCIMONAS LEMOIGNEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsHermawan, S. / Subedi, B. / Papageorgiou, A.C. / Jendrossek, D.
Citation
Journal: Mol.Microbiol. / Year: 2013
Title: Biochemical Analysis and Structure Determination of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase Phaz7 Muteins Reveal the Phb Binding Site and Details of Substrate-Enzyme Interactions.
Authors: Jendrossek, D. / Hermawan, S. / Subedi, B. / Papageorgiou, A.C.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Structural Basis of Poly(3-Hydroxybutyrate) Hydrolysis by Phaz7 Depolymerase from Paucimonas Lemoignei.
Authors: Papageorgiou, A.C. / Hermawan, S. / Singh, C.B. / Jendrossek, D.
History
DepositionJun 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHB DEPOLYMERASE PHAZ7
B: PHB DEPOLYMERASE PHAZ7
C: PHB DEPOLYMERASE PHAZ7
D: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)141,1324
Polymers141,1324
Non-polymers00
Water32,4811803
1
A: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)35,2831
Polymers35,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)35,2831
Polymers35,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)35,2831
Polymers35,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHB DEPOLYMERASE PHAZ7


Theoretical massNumber of molelcules
Total (without water)35,2831
Polymers35,2831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.239, 138.829, 172.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2205-

HOH

21C-2176-

HOH

31D-2417-

HOH

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Components

#1: Protein
PHB DEPOLYMERASE PHAZ7


Mass: 35282.934 Da / Num. of mol.: 4 / Fragment: RESIDUES 39-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAUCIMONAS LEMOIGNEI (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): WB800
References: UniProt: Q939Q9, poly(3-hydroxybutyrate) depolymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1803 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 202-208 HAVE BEEN DELETED

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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 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN CONCENTRATION 10 MG/ML. 0.1 M NAOAC (PH 5.0), 0.2 M LICL, 15% W/V PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2→19.6 Å / Num. obs: 74317 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.4 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BRS

4brs


Resolution: 2.002→19.558 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 3711 5 %
Rwork0.1152 --
obs0.119 74248 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.7 Å2
Refinement stepCycle: LAST / Resolution: 2.002→19.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9916 0 0 1803 11719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310237
X-RAY DIFFRACTIONf_angle_d1.31913883
X-RAY DIFFRACTIONf_dihedral_angle_d12.5443487
X-RAY DIFFRACTIONf_chiral_restr0.0761470
X-RAY DIFFRACTIONf_plane_restr0.0071814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0024-2.02770.23821080.16842048X-RAY DIFFRACTION78
2.0277-2.05440.2561360.13272601X-RAY DIFFRACTION100
2.0544-2.08250.22041380.12362619X-RAY DIFFRACTION100
2.0825-2.11220.20641390.12182633X-RAY DIFFRACTION100
2.1122-2.14370.19711370.11652605X-RAY DIFFRACTION100
2.1437-2.17720.20361380.11822628X-RAY DIFFRACTION100
2.1772-2.21280.21981380.11142612X-RAY DIFFRACTION100
2.2128-2.25090.1771380.11132621X-RAY DIFFRACTION100
2.2509-2.29180.22051370.10852603X-RAY DIFFRACTION100
2.2918-2.33580.18321400.10472659X-RAY DIFFRACTION100
2.3358-2.38340.2121370.10422619X-RAY DIFFRACTION100
2.3834-2.43510.19071370.10522604X-RAY DIFFRACTION100
2.4351-2.49170.18971390.11422628X-RAY DIFFRACTION100
2.4917-2.55380.22181390.1142654X-RAY DIFFRACTION100
2.5538-2.62270.19471390.11062629X-RAY DIFFRACTION100
2.6227-2.69970.19561390.11272653X-RAY DIFFRACTION100
2.6997-2.78660.18311390.11382628X-RAY DIFFRACTION100
2.7866-2.88590.19751380.1192635X-RAY DIFFRACTION100
2.8859-3.00110.1991380.11812637X-RAY DIFFRACTION100
3.0011-3.13710.16011390.11832638X-RAY DIFFRACTION100
3.1371-3.30180.21511390.12262643X-RAY DIFFRACTION100
3.3018-3.50750.20721400.11712648X-RAY DIFFRACTION100
3.5075-3.77660.18151390.11052650X-RAY DIFFRACTION99
3.7766-4.15330.14751400.10042661X-RAY DIFFRACTION99
4.1533-4.74680.15821400.0942645X-RAY DIFFRACTION99
4.7468-5.95240.1351400.11282687X-RAY DIFFRACTION98
5.9524-19.5590.20421400.15822649X-RAY DIFFRACTION95

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