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- PDB-4bym: Structure of PhaZ7 PHB depolymerase Y105E mutant -

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Basic information

Entry
Database: PDB / ID: 4bym
TitleStructure of PhaZ7 PHB depolymerase Y105E mutant
ComponentsPHB DEPOLYMERASE PHAZ7
KeywordsHYDROLASE / CATALYTIC TRIAD / SUBSTRATE-BINDING CAVITY / BINDING CAVITY / 3HB TRIMER BINDING
Function / homology
Function and homology information


lipid catabolic process / hydrolase activity
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: 1.598 Å
AuthorsHermawan, S. / Subedi, B. / Papageorgiou, A.C. / Jendrossek, D.
CitationJournal: 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.
History
DepositionJul 20, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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
B: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4875
Polymers72,4062
Non-polymers813
Water21,7981210
1
A: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2262
Polymers36,2031
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHB DEPOLYMERASE PHAZ7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2613
Polymers36,2031
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.560, 200.340, 44.520
Angle α, β, γ (deg.)90.00, 114.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHB DEPOLYMERASE PHAZ7 / PHB DEPOLYMERASE


Mass: 36202.945 Da / Num. of mol.: 2 / Mutation: YES
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.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1210 / 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: 2.3 Å3/Da / Density % sol: 43 % / 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, 18% 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 / 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: 1.6→20 Å / Num. obs: 85362 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.9 / % possible all: 95.5

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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: 1.598→19.843 Å / SU ML: 0.16 / σ(F): 1.99 / Phase error: 16.24 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1743 4266 5 %
Rwork0.1484 --
obs0.1497 85301 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.8 Å2
Refinement stepCycle: LAST / Resolution: 1.598→19.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 3 1210 6292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085335
X-RAY DIFFRACTIONf_angle_d1.0377261
X-RAY DIFFRACTIONf_dihedral_angle_d12.1991843
X-RAY DIFFRACTIONf_chiral_restr0.07768
X-RAY DIFFRACTIONf_plane_restr0.005943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5981-1.61630.28931140.24522161X-RAY DIFFRACTION80
1.6163-1.63530.28151430.22152707X-RAY DIFFRACTION100
1.6353-1.65520.21581480.20542813X-RAY DIFFRACTION99
1.6552-1.67620.23221410.19272694X-RAY DIFFRACTION100
1.6762-1.69820.22351440.18222738X-RAY DIFFRACTION100
1.6982-1.72140.19761470.18242786X-RAY DIFFRACTION99
1.7214-1.7460.23041400.17272661X-RAY DIFFRACTION100
1.746-1.77210.18841460.17022768X-RAY DIFFRACTION99
1.7721-1.79970.18131450.16752762X-RAY DIFFRACTION99
1.7997-1.82920.19541410.16832668X-RAY DIFFRACTION100
1.8292-1.86070.20911480.16412823X-RAY DIFFRACTION99
1.8607-1.89460.21451410.16652666X-RAY DIFFRACTION99
1.8946-1.9310.20481440.16052749X-RAY DIFFRACTION100
1.931-1.97030.19121440.15542722X-RAY DIFFRACTION99
1.9703-2.01320.15351450.14942755X-RAY DIFFRACTION100
2.0132-2.05990.20151420.14792710X-RAY DIFFRACTION99
2.0599-2.11140.1851450.14812747X-RAY DIFFRACTION99
2.1114-2.16840.19851410.14382687X-RAY DIFFRACTION99
2.1684-2.23210.17261450.14372747X-RAY DIFFRACTION99
2.2321-2.30410.18681430.14492728X-RAY DIFFRACTION98
2.3041-2.38630.1761430.14622702X-RAY DIFFRACTION99
2.3863-2.48170.171430.14422729X-RAY DIFFRACTION98
2.4817-2.59440.1521440.1422730X-RAY DIFFRACTION98
2.5944-2.73080.16911410.14282689X-RAY DIFFRACTION99
2.7308-2.90150.16261430.14162713X-RAY DIFFRACTION98
2.9015-3.12470.15751420.1432692X-RAY DIFFRACTION98
3.1247-3.43770.14121420.1372709X-RAY DIFFRACTION98
3.4377-3.93170.13851400.12412655X-RAY DIFFRACTION97
3.9317-4.94090.14261400.11582661X-RAY DIFFRACTION96
4.9409-19.84480.14651410.1372663X-RAY DIFFRACTION95

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