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- PDB-4brs: Structure of wild type PhaZ7 PHB depolymerase -

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Basic information

Entry
Database: PDB / ID: 4brs
TitleStructure of wild type 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: 1.6 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 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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 / 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 / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8317
Polymers72,7022
Non-polymers1295
Water20,0691114
1
A: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3983
Polymers36,3511
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4334
Polymers36,3511
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.400, 199.700, 44.200
Angle α, β, γ (deg.)90.00, 114.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHB DEPOLYMERASE PHAZ7


Mass: 36351.109 Da / Num. of mol.: 2
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / 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: 2.17 Å3/Da / Density % sol: 43.24 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M NAOAC (PH 5.0), 0.2 M MGCL2 AND 18 % W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.6→21.92 Å / Num. obs: 81064 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 11.06 Å2 / Rmerge(I) obs: 0.02 / Net I/σ(I): 27.39
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.63 / % possible all: 81.2

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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 2VTV

2vtv


Resolution: 1.6→21.923 Å / SU ML: 0.15 / σ(F): 2.05 / Phase error: 15.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 4053 5 %
Rwork0.1317 --
obs0.1336 81057 94.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→21.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5008 0 5 1114 6127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125182
X-RAY DIFFRACTIONf_angle_d1.2827037
X-RAY DIFFRACTIONf_dihedral_angle_d12.31752
X-RAY DIFFRACTIONf_chiral_restr0.078743
X-RAY DIFFRACTIONf_plane_restr0.007913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61880.2361070.17552031X-RAY DIFFRACTION74
1.6188-1.63860.20781300.16852455X-RAY DIFFRACTION88
1.6386-1.65930.21861330.16182537X-RAY DIFFRACTION89
1.6593-1.68110.19361300.15462476X-RAY DIFFRACTION90
1.6811-1.70420.20291360.15632568X-RAY DIFFRACTION91
1.7042-1.72850.19991350.15432583X-RAY DIFFRACTION91
1.7285-1.75430.20311370.15982587X-RAY DIFFRACTION94
1.7543-1.78170.1941380.15042638X-RAY DIFFRACTION94
1.7817-1.81090.21061400.15412652X-RAY DIFFRACTION95
1.8109-1.84210.20981420.14892699X-RAY DIFFRACTION95
1.8421-1.87560.19171400.14512664X-RAY DIFFRACTION96
1.8756-1.91160.18311430.14312711X-RAY DIFFRACTION97
1.9116-1.95060.16421420.13692701X-RAY DIFFRACTION96
1.9506-1.9930.17541460.13762766X-RAY DIFFRACTION98
1.993-2.03930.17141430.13582726X-RAY DIFFRACTION98
2.0393-2.09030.17891450.13662752X-RAY DIFFRACTION98
2.0903-2.14680.18151440.12922741X-RAY DIFFRACTION98
2.1468-2.20990.16451480.12262812X-RAY DIFFRACTION99
2.2099-2.28110.14791410.12232677X-RAY DIFFRACTION97
2.2811-2.36260.18471440.12442733X-RAY DIFFRACTION97
2.3626-2.45710.16941480.12642817X-RAY DIFFRACTION98
2.4571-2.56870.16411430.12332710X-RAY DIFFRACTION97
2.5687-2.70390.17561420.11712705X-RAY DIFFRACTION97
2.7039-2.8730.14651440.12132730X-RAY DIFFRACTION97
2.873-3.09420.16711440.12412737X-RAY DIFFRACTION97
3.0942-3.40460.17281440.11962735X-RAY DIFFRACTION97
3.4046-3.89490.14531400.11562662X-RAY DIFFRACTION95
3.8949-4.89810.12891410.11062670X-RAY DIFFRACTION94
4.8981-21.92460.17131430.15912729X-RAY DIFFRACTION96

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