[English] 日本語
Yorodumi
- PDB-2v3w: Crystal structure of the benzoylformate decarboxylase variant L46... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v3w
TitleCrystal structure of the benzoylformate decarboxylase variant L461A from Pseudomonas putida
ComponentsBENZOYLFORMATE DECARBOXYLASE
KeywordsLYASE / CALCIUM / MAGNESIUM / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE / RATIONAL PROTEIN DESIGN / AROMATIC HYDROCARBONS CATABOLISM / THDP-DEPENDENT / MANDELATE PATHWAY / METAL-BINDING / DECARBOXYLASE / CARBOLIGATION
Function / homology
Function and homology information


benzoylformate decarboxylase / benzoylformate decarboxylase activity / mandelate catabolic process / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains ...Thiamine pyrophosphate enzyme / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Benzoylformate decarboxylase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGocke, D. / Walter, L. / Gauchenova, K. / Kolter, G. / Knoll, M. / Berthold, C.L. / Schneider, G. / Pleiss, J. / Mueller, M. / Pohl, M.
CitationJournal: Chembiochem / Year: 2008
Title: Rational Protein Design of Thdp-Dependent Enzymes-Engineering Stereoselectivity.
Authors: Gocke, D. / Walter, L. / Gauchenova, K. / Kolter, G. / Knoll, M. / Berthold, C.L. / Schneider, G. / Pleiss, J. / Muller, M. / Pohl, M.
History
DepositionJun 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BENZOYLFORMATE DECARBOXYLASE
B: BENZOYLFORMATE DECARBOXYLASE
C: BENZOYLFORMATE DECARBOXYLASE
D: BENZOYLFORMATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,67418
Polymers225,4434
Non-polymers2,23114
Water17,096949
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27590 Å2
ΔGint-285.8 kcal/mol
Surface area58760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.704, 139.938, 169.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.06624, 0.65135, 0.75588), (0.65313, -0.54441, 0.52635), (0.75435, 0.52855, -0.38935)89.98735, -53.99818, -64.6412
2given(-0.37109, 0.15442, -0.91567), (0.162, -0.96019, -0.22758), (-0.91436, -0.23279, 0.3313)26.24144, -74.31826, 5.14572
3given(-0.56469, -0.80869, 0.16475), (-0.80983, 0.50447, -0.29948), (0.15907, -0.30254, -0.93977)44.06684, 6.45169, -86.10317

-
Components

#1: Protein
BENZOYLFORMATE DECARBOXYLASE / BFD / BFDC


Mass: 56360.668 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Plasmid: PKK233-2/BFDL461A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / Variant (production host): PREP4 / References: UniProt: P20906, benzoylformate decarboxylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 949 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 461 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 461 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, LEU 461 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 461 TO ALA ENGINEERED RESIDUE IN CHAIN C, LEU 461 TO ALA ENGINEERED RESIDUE IN CHAIN D, LEU 461 TO ALA
Sequence detailsRESIDUE 461 HAS BEEN POINT MUTATED FROM LEUCINE INTO ALANINE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 20, 2006 / Details: RH-COATED SI MIRROR, RH- COATED TOROIDAL SI MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111). / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→107.8 Å / Num. obs: 111569 / % possible obs: 97 % / Observed criterion σ(I): 6 / Redundancy: 2.9 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BFD

1bfd


Resolution: 2.2→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.879 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5610 5 %RANDOM
Rwork0.18 ---
obs0.182 105886 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.37 Å20 Å20 Å2
2---1.4 Å20 Å2
3----1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15780 0 130 949 16859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02216358
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210649
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.96922397
X-RAY DIFFRACTIONr_angle_other_deg0.858326080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85252118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65224.43693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.425152408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0661592
X-RAY DIFFRACTIONr_chiral_restr0.0610.22497
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023113
X-RAY DIFFRACTIONr_nbd_refined0.1910.23408
X-RAY DIFFRACTIONr_nbd_other0.1840.211613
X-RAY DIFFRACTIONr_nbtor_refined0.1680.28092
X-RAY DIFFRACTIONr_nbtor_other0.0840.28391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2967
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.914313510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.028316936
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37246690
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it255452
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 430
Rwork0.237 7960

+
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://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