[English] 日本語
Yorodumi
- PDB-3ud6: Structural analyses of covalent enzyme-substrate analogue complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ud6
TitleStructural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design
ComponentsRETRO-ALDOLASE
KeywordsLYASE/LYASE INHIBITOR / Computationally Designed / Retroaldolase / Tim Barrel / LYASE-LYASE INHIBITOR complex
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.091 Å
AuthorsBaker, D. / Stoddard, B.L. / Althoff, E.A. / Wang, L. / Jiang, L. / Moody, J. / Bolduc, J. / Lassila, J. / Hilvert, D.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
Authors: Wang, L. / Althoff, E.A. / Bolduc, J. / Jiang, L. / Moody, J. / Lassila, J.K. / Giger, L. / Hilvert, D. / Stoddard, B. / Baker, D.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionNov 23, 2011ID: 3NL8
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Feb 1, 2012Group: Database references / Non-polymer description
Revision 1.3Nov 20, 2013Group: Non-polymer description
Revision 1.4Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_bond.pdbx_aromatic_flag / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RETRO-ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1714
Polymers29,7361
Non-polymers4343
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.684, 62.684, 123.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein RETRO-ALDOLASE


Mass: 29736.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The Sequence Was Computationally Designed Based On Indole 3 Glycerol Phosphate Synthase Naturally Found in Sulfolobus Solfataricus.
Source: (gene. exp.) ARTIFICIAL GENE (others)
Description: THE SEQUENCE WAS COMPUTATIONALLY DESIGNED BASED ON INDOLE-3-GLYCEROL PHOSPHATE SYNTHASE NATURALLY FOUND IN SULFOLOBUS SOLFATARICUS.
Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-3NK / 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE


Mass: 242.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details1-(6-METHOXY-2-NAPTHALENYL)-1,3-BUTANEDIONE (3NK) WAS REACTED WITH THE PROTEIN AND QUENCHED WITH ...1-(6-METHOXY-2-NAPTHALENYL)-1,3-BUTANEDIONE (3NK) WAS REACTED WITH THE PROTEIN AND QUENCHED WITH NA(BN)CH3. THE RESULTING COMPLEX FORMS A DOUBLE BOND BETWEEN ATOM C13 OF 3NK AND NZ OF LYS 159

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: Protein at 5mg/ml in 100mm NaCl, 25mm TRIS pH7.5. Crystals grew at and near 2M ammonium sulfate, 4% PEG400, 100mN Na acetate pH5.5, vapor diffusion, temperature 298k, VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 18, 2009 / Details: VARIMAX HF
RadiationMonochromator: VARIMAX HR MIRRORS/OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.091→50 Å / Num. obs: 17137 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 29.82 Å2 / Rsym value: 0.037 / Net I/σ(I): 22
Reflection shellResolution: 2.091→2.16 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 6.86 / Rsym value: 0.153 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A53, MODIFIED TO PREVENT MODEL BIAS

1a53


Resolution: 2.091→19.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.894 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 868 5.1 %RANDOM
Rwork0.227 ---
obs0.227 16229 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å / Luzzati d res low obs: 19.47 Å
Refinement stepCycle: LAST / Resolution: 2.091→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 27 65 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0282.0032749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.43923.8289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26815384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7781519
X-RAY DIFFRACTIONr_chiral_restr0.0660.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021484
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.2902
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2119
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.76521285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37632011
X-RAY DIFFRACTIONr_scbond_it1.9084871
X-RAY DIFFRACTIONr_scangle_it3.2156738
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.091→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 53 -
Rwork0.246 1121 -
obs--96.71 %

+
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