[English] 日本語
Yorodumi
- PDB-4wcv: Haloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wcv
TitleHaloalkane dehalogenase DhaA mutant from Rhodococcus rhodochrous (T148L+G171Q+A172V+C176G)
ComponentsHaloalkane dehalogenase
KeywordsHYDROLASE / mutation in tunnel access
Function / homology
Function and homology information


haloalkane dehalogenase / haloalkane dehalogenase activity / response to toxic substance / membrane
Similarity search - Function
Haloalkane dehalogenase, subfamily 2 / : / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Haloalkane dehalogenase / Haloalkane dehalogenase
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHolubeva, T. / Prudnikova, T. / Kuta-Smatanova, I. / Rezacova, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicP207/12/0775 Czech Republic
CitationJournal: Chemcatchem / Year: 2015
Title: Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels
Authors: Liskova, V. / Bednar, D. / Prudnikova, T. / Rezacova, P. / Koudelakova, T. / Sebestova, E. / Kuta-Smatanova, I. / Brezovsky, J. / Chaloupkova, R. / Damborsky, J.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Haloalkane dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4805
Polymers34,1761
Non-polymers3044
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-11 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.585, 44.477, 46.508
Angle α, β, γ (deg.)115.47, 98.79, 109.12
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Haloalkane dehalogenase


Mass: 34175.961 Da / Num. of mol.: 1 / Mutation: T148L+G171Q+A172V+C176G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: dhaA / Plasmid: pAQN / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A3G3, UniProt: P0A3G2*PLUS, haloalkane dehalogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: sodium acetate trihydrate, ammonium acetate, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.69→39.42 Å / Num. all: 30835 / Num. obs: 28416 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 18.76
Reflection shellResolution: 1.69→1.73 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.16 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G9X

3g9x


Resolution: 1.69→39.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.179 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17573 1421 5 %RANDOM
Rwork0.12015 ---
obs0.12295 26995 92.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20.01 Å2
2--0.03 Å20.01 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.69→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2365 0 19 477 2861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9593510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9223.566129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5481518
X-RAY DIFFRACTIONr_chiral_restr0.1370.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0222061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1030.6951210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4081520
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2440.7981347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.4494567
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.11232531
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded10.69652436
LS refinement shellResolution: 1.689→1.733 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 99 -
Rwork0.114 1882 -
obs--87.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.0941-0.0263-0.04140.07280.01270.08770.00250.0065-0.0028-0.0024-0.00380.0099-0.0005-0.00770.00130.0146-0.0075-0.01070.00490.0050.0088Chain A 4-132 residua-5.0761.49-6.656
20.25450.36810.34360.53930.49130.4698-0.02650.0105-0.0039-0.05170.0252-0.0091-0.02760.01020.00140.026-0.00770.00560.01780.00180.013Chain A 133-144 residua6.512-8.96714.484
30.23-0.3543-0.23840.59150.35450.2655-0.0149-0.0132-0.00220.02690.00720.00780.00850.00870.00770.0197-0.0032-0.00970.01740.00280.0106Chain A 145-158 residua-0.35-0.46420.143
40.8467-0.3209-0.43560.15870.13360.2509-0.0062-0.0330.02310.00350.0105-0.0195-0.00110.0173-0.00420.0179-0.005-0.00640.00790.00350.007Chain A 159-167 residua-5.2899.03818.027
50.3429-0.1738-0.07340.14390.10660.1033-0.007-0.01590.01540.00290.0106-0.0113-0.00420.0087-0.00370.0175-0.0101-0.01210.00890.00250.0163Chain A 168-185 residua7.29711.6447.67
60.45480.0982-0.45380.6742-0.03860.51090.01550.02450.03140.00910.00820.0147-0.0104-0.0065-0.02370.0195-0.0041-0.00980.00940.00760.01Chain A 186-196 residua-3.29815.6275.73
70.059-0.0146-0.04730.29710.04860.0915-0.0010.0034-0.0120.0065-0.00810.01810.0056-0.00210.00920.0159-0.0074-0.00990.00680.00630.0123Chain A 197-230 residua-4.793-7.6337.796
80.01170.04710.01320.32660.11810.1324-0.0048-0.0065-0.00260.0150.007-0.00610.02270.0092-0.00220.020.001-0.00790.01750.0070.0126Chain A 231-263 residua11.4-11.143-1.972
90.12780.0108-0.0120.08740.10340.23710.0053-0.0047-0.006-0.00770.0028-0.0151-0.00370.0081-0.00810.0167-0.006-0.00940.00490.0050.0117Chain A 264-295 residua11.201-0.574-7.994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 132
2X-RAY DIFFRACTION2A133 - 144
3X-RAY DIFFRACTION3A145 - 158
4X-RAY DIFFRACTION4A159 - 167
5X-RAY DIFFRACTION5A168 - 185
6X-RAY DIFFRACTION6A186 - 196
7X-RAY DIFFRACTION7A197 - 230
8X-RAY DIFFRACTION8A231 - 263
9X-RAY DIFFRACTION9A264 - 295

+
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