[English] 日本語
Yorodumi
- PDB-4bvl: Structure of 202-208 deletion mutant of PhaZ7 PHB depolymerase -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Sequence detailsRESIDUES 202-208 HAVE BEEN DELETED

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more