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- PDB-4czd: Sirohaem decarboxylase AhbA/B - an enzyme with structural homolog... -

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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 / sequence-specific DNA binding / lyase activity
Similarity search - Function
Siroheme decarboxylase , AsnC-like ligand binding domain / AsnC-like ligand binding domain / AsnC-type helix-turn-helix domain / AsnC-type HTH 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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