[English] 日本語
Yorodumi
- PDB-4ntd: Crystal structure of HlmI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ntd
TitleCrystal structure of HlmI
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / disulfide bond / natural sulfur products / holomycin
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / GLUTATHIONE / PHOSPHATE ION / Thioredoxin reductase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsScharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products
Authors: Scharf, D.H. / Groll, M. / Habel, A. / Heinekamp, T. / Hertweck, C. / Brakhage, A.A. / Huber, E.M.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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_conn.pdbx_leaving_atom_flag / _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: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3026
Polymers35,9861
Non-polymers1,3155
Water7,909439
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,60412
Polymers71,9732
Non-polymers2,63110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6870 Å2
ΔGint-39 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 96.350, 133.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-405-

PO4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin reductase


Mass: 35986.422 Da / Num. of mol.: 1 / Fragment: UNP residues 29-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Strain: ATCC 27064 / Gene: SCLAV_5275 / Plasmid: pET43.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E2PZ87

-
Non-polymers , 6 types, 444 molecules

#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 1.3M Na/K phosphate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 94912 / Num. obs: 93867 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FK1

4fk1


Resolution: 1.6→10 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.93 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15938 4694 5 %RANDOM
Rwork0.14645 ---
all0.149 93867 --
obs0.1471 89173 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.809 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.13 Å20 Å2
2--0.13 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 85 439 2888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192654
X-RAY DIFFRACTIONr_bond_other_d0.0030.022564
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9953630
X-RAY DIFFRACTIONr_angle_other_deg0.8823.0035856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.17321.066122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94315419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611544
X-RAY DIFFRACTIONr_chiral_restr0.0630.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_rigid_bond_restr2.39735217
X-RAY DIFFRACTIONr_sphericity_free27.821577
X-RAY DIFFRACTIONr_sphericity_bonded11.79855526
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 341 -
Rwork0.284 6465 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 19.6493 Å / Origin y: 38.7667 Å / Origin z: 13.1581 Å
111213212223313233
T0.0169 Å20.0009 Å20.0007 Å2-0.0157 Å2-0.0005 Å2--0.0004 Å2
L0.054 °2-0.0305 °20.0153 °2-0.0227 °2-0.0166 °2--0.024 °2
S-0.0065 Å °-0.004 Å °-0.0025 Å °0.0065 Å °0.0052 Å °0.001 Å °0.0001 Å °-0.0033 Å °0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 318
2X-RAY DIFFRACTION1A401 - 402

+
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