[English] 日本語
Yorodumi
- PDB-4czd: Sirohaem decarboxylase AhbA/B - an enzyme with structural homolog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4czd
TitleSirohaem decarboxylase AhbA/B - an enzyme with structural homology to the Lrp/AsnC transcription factor family that is part of the alternative haem biosynthesis pathway.
Components(PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY) x 2
KeywordsLYASE
Function / homology
Function and homology information


siroheme decarboxylase / heme biosynthetic process / lyase activity
Similarity search - Function
Siroheme decarboxylase , AsnC-like ligand binding domain / : / AsnC-like ligand binding domain / Siroheme decarboxylase NirDL-like HTH domain / AsnC-type helix-turn-helix domain / : / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Siroheme decarboxylase alpha subunit / Siroheme decarboxylase beta subunit
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å
AuthorsPalmer, D.J. / Brown, D.G. / Warren, M.J.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: The Structure, Function and Properties of Sirohaem Decarboxylase - an Enzyme with Structural Homology to a Transcription Factor Family that is Part of the Alternative Haem Biosynthesis Pathway.
Authors: Palmer, D.J. / Schroeder, S. / Lawrence, A.D. / Deery, E. / Lobo, S.A. / Saraiva, L.M. / Mclean, K.J. / Munro, A.W. / Ferguson, S.J. / Pickersgill, R.W. / Brown, D.G. / Warren, M.J.
History
DepositionApr 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
B: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
C: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
D: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY


Theoretical massNumber of molelcules
Total (without water)78,6514
Polymers78,6514
Non-polymers00
Water4,540252
1
A: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
B: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY


Theoretical massNumber of molelcules
Total (without water)39,3262
Polymers39,3262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-34.8 kcal/mol
Surface area15330 Å2
MethodPISA
2
C: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY
D: PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY


Theoretical massNumber of molelcules
Total (without water)39,3262
Polymers39,3262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-29.6 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.850, 78.620, 151.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY / AHBA DECARBOXYLASE A CHAIN


Mass: 19212.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO DESULFURICANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J364
#2: Protein PUTATIVE TRANSCRIPTIONAL REGULATOR, ASNC FAMILY / AHBB DECARBOXYLASE B CHAIN


Mass: 20112.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO DESULFURICANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J3A4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5
Details: 26% PEG4K, 0.2M AMMONIUM ACETATE, 0.1M NA ACETATE PH 5.0, 0.01M BACL

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONDiamond I04-110.92
SYNCHROTRONDiamond I0220.97917, 0.97935, 0.9854
Detector
TypeIDDetectorDate
DECTRIS PILATUS 2M1PIXELDec 9, 2013
DECTRIS PILATUS 6M2PIXEL
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.979171
30.979351
40.98541
ReflectionResolution: 2.23→69.8 Å / Num. obs: 32358 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 42.83 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
Aimlessdata scaling
SOLVE-RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.23→69.77 Å / Cor.coef. Fo:Fc: 0.9364 / Cor.coef. Fo:Fc free: 0.9153 / SU R Cruickshank DPI: 0.278 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.292 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.207
Details: DISORDER LINKER FOR MOLECULE B RESIDUES 62-68 WERE MODELLED BASED ON MOLECULE D AND INCLUDED FOR CLARITY THERE IS NCS BUT FOR TIME REASONS THE DETAILS WERE NOT INCLUDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 1642 5.08 %RANDOM
Rwork0.1975 ---
obs0.1994 32323 97.09 %-
Displacement parametersBiso mean: 39.51 Å2
Baniso -1Baniso -2Baniso -3
1--3.353 Å20 Å20 Å2
2--0.5809 Å20 Å2
3---2.7721 Å2
Refine analyzeLuzzati coordinate error obs: 0.289 Å
Refinement stepCycle: LAST / Resolution: 2.23→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 0 252 4940
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014782HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1679SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes695HARMONIC5
X-RAY DIFFRACTIONt_it4782HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion19.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion633SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5249SEMIHARMONIC4
LS refinement shellResolution: 2.23→2.3 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2527 126 4.67 %
Rwork0.2397 2572 -
all0.2403 2698 -
obs--97.09 %

+
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