[English] 日本語
Yorodumi
- PDB-3cgb: Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cgb
TitlePyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity
ComponentsPyridine nucleotide-disulfide oxidoreductase, class I
KeywordsOXIDOREDUCTASE / coenzyme A / flavin adenine dinucleotide / selenomethionine / FAD / Flavoprotein
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...: / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / FLAVIN-ADENINE DINUCLEOTIDE / Pyridine nucleotide-disulfide oxidoreductase, class I / Pyridine nucleotide-disulfide oxidoreductase, class I
Similarity search - Component
Biological speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsWallen, J.R.
CitationJournal: Biochemistry / Year: 2008
Title: Pyridine Nucleotide Complexes with Bacillus anthracis Coenzyme A-Disulfide Reductase: A Structural Analysis of Dual NAD(P)H Specificity.
Authors: Wallen, J.R. / Paige, C. / Mallett, T.C. / Karplus, P.A. / Claiborne, A.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridine nucleotide-disulfide oxidoreductase, class I
B: Pyridine nucleotide-disulfide oxidoreductase, class I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8566
Polymers108,7502
Non-polymers3,1064
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-34.3 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.258, 80.763, 98.370
Angle α, β, γ (deg.)90.00, 103.98, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Pyridine nucleotide-disulfide oxidoreductase, class I


Mass: 54375.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: pyridine nucleotide-disulfide oxidoreductase, class I / Plasmid: pTrcHisC / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q81TK8, UniProt: A0A6L7HMK7*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16-26% 2-methyl-2,4-pentanediol, 0.2 M magnesium acetate, 0.1 M sodium cacodylate, pH 6.5, and 2 mM NAD(P)+, VAPOR DIFFUSION, SITTING DROP, temperature 288K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C10.9791
SYNCHROTRONNSLS X26C20.9796
SYNCHROTRONNSLS X26C30.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2004
RadiationMonochromator: channel-cut Si(111) crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97961
30.951
ReflectionResolution: 1.9→38.22 Å / Num. all: 200403 / Num. obs: 195454 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.85 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.9 / Num. unique all: 20110 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
d*TREKdata reduction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→38.22 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.754 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.22976 5014 5 %RANDOM
Rwork0.19909 ---
obs0.20064 94336 97.43 %-
all-96824 --
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: 33.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å2-0.98 Å2
2--1.93 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6958 0 202 551 7711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227363
X-RAY DIFFRACTIONr_angle_refined_deg1.4922.00110013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69424.769325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.977151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9161540
X-RAY DIFFRACTIONr_chiral_restr0.0990.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025424
X-RAY DIFFRACTIONr_nbd_refined0.2090.23389
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2625
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.213
X-RAY DIFFRACTIONr_mcbond_it0.94834513
X-RAY DIFFRACTIONr_mcangle_it1.4647142
X-RAY DIFFRACTIONr_scbond_it2.38863331
X-RAY DIFFRACTIONr_scangle_it3.89492862
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 379 -
Rwork0.305 6843 -
obs-6843 96.28 %

+
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