[English] 日本語
Yorodumi
- PDB-4ixt: Structure of a 37-fold mutant of halohydrin dehalogenase (HheC) b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ixt
TitleStructure of a 37-fold mutant of halohydrin dehalogenase (HheC) bound to ethyl (R)-4-cyano-3-hydroxybutyrate
ComponentsHalohydrin dehalogenase
KeywordsLYASE / thermostability / synergistic mutations / coupled mutations / proline-induced / backbone changes / enantioselectivity changes / directed evolution / protein engineering / short-chain dehydrogenase/reductase enzyme superfamily / Cyanolysis / dehalogenase / Atorvastatin synthesis
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ethyl (3R)-4-cyano-3-hydroxybutanoate / Halohydrin dehalogenase
Function and homology information
Biological speciesRhizobium radiobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsFloor, R.J. / Schallmey, M. / Hauer, B. / Breuer, M. / Jekel, P.A. / Wijma, H.J. / Dijkstra, B.W. / Janssen, D.B.
CitationJournal: Chembiochem / Year: 2013
Title: Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase.
Authors: Schallmey, M. / Floor, R.J. / Hauer, B. / Breuer, M. / Jekel, P.A. / Wijma, H.J. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Halohydrin dehalogenase
B: Halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8754
Polymers55,6832
Non-polymers1932
Water97354
1
A: Halohydrin dehalogenase
B: Halohydrin dehalogenase
hetero molecules

A: Halohydrin dehalogenase
B: Halohydrin dehalogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7518
Polymers111,3664
Non-polymers3854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16080 Å2
ΔGint-129 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.682, 104.682, 121.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Halohydrin dehalogenase /


Mass: 27841.406 Da / Num. of mol.: 2 / Fragment: Halohydrin dehalogenase HheC
Mutation: Q37H, K38Q, K52I, A60V, Y70L, Q72H, V75I, F82A, A83P, P84V, F86W, Q87R, G99D, A100M, R107K, V112A, K121R, T134A, P135S, T146A, C153S, T154A, Y166H, G174A, Y177G, L178V, H179D, E181G, F186Y, ...Mutation: Q37H, K38Q, K52I, A60V, Y70L, Q72H, V75I, F82A, A83P, P84V, F86W, Q87R, G99D, A100M, R107K, V112A, K121R, T134A, P135S, T146A, C153S, T154A, Y166H, G174A, Y177G, L178V, H179D, E181G, F186Y, T189S, N195S, V201W, K203R, V205Y, A222T, M245V, I246V
Source method: isolated from a genetically manipulated source
Details: This enzyme is a result of a directed evolution study. It contains 37 mutations, compared to its parent
Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: hheC / Plasmid: pBAD-HheC-2360 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q93D82, Lyases; Carbon-halide lyases
#2: Chemical ChemComp-1H1 / ethyl (3R)-4-cyano-3-hydroxybutanoate


Mass: 157.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO3
#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.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5% (w/v) PEG 8000,0.2 M Magnesium Chloride, 0.1 M Tris-Cl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2010
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.47→73.36 Å / Num. obs: 27496 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 7.3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PWZ

1pwz


Resolution: 2.49→52.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.415 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.364 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24895 1233 5.1 %RANDOM
Rwork0.19945 ---
all0.26 22989 --
obs0.20192 22989 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.067 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2---0.05 Å2-0 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.49→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 12 54 3877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223924
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9485344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1365492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39424.142169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.20615606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9941517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213011
X-RAY DIFFRACTIONr_mcbond_it1.2861.52464
X-RAY DIFFRACTIONr_mcangle_it2.30423958
X-RAY DIFFRACTIONr_scbond_it3.78531460
X-RAY DIFFRACTIONr_scangle_it6.0064.51386
LS refinement shellResolution: 2.49→2.553 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 77 -
Rwork0.242 1682 -
obs-3471 100 %

+
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