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- PDB-4ccs: The structure of CbiX, the terminal Enzyme for Biosynthesis of Si... -

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Basic information

Entry
Database: PDB / ID: 4ccs
TitleThe structure of CbiX, the terminal Enzyme for Biosynthesis of Siroheme in Denitrifying Bacteria
ComponentsCBIXSirohydrochlorin cobaltochelatase
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


sirohydrochlorin cobaltochelatase activity / cobalamin biosynthetic process / metal ion binding
Similarity search - Function
Sirohydrochlorin cobaltochelatase CbiX-like / CbiX / Rossmann fold - #1400 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPARACOCCUS PANTOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsBali, S. / Rollauer, S.E. / Roversi, P. / Raux-Deery, E. / Lea, S.M. / Warren, M.J. / Ferguson, S.J.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: Identification and Characterization of the 'Missing' Terminal Enzyme for Siroheme Biosynthesis in Alpha-Proteobacteria.
Authors: Bali, S. / Rollauer, S. / Roversi, P. / Raux-Deery, E. / Lea, S.M. / Warren, M.J. / Ferguson, S.J.
History
DepositionOct 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBIX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1624
Polymers23,9431
Non-polymers2193
Water4,288238
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.450, 130.450, 56.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-309-

NA

21A-2071-

HOH

31A-2104-

HOH

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Components

#1: Protein CBIX / Sirohydrochlorin cobaltochelatase


Mass: 23942.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PARACOCCUS PANTOTROPHUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: A0A023GPI5*PLUS
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.68 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.2M IMIDAZOLE MALATE PH 5.5, 24% PEG 600

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11931
21931
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID2910.8726
SYNCHROTRONDiamond I04-120.9173
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 2M1PIXELSep 10, 2011MIRRORS
DECTRIS PILATUS 2M2PIXELOct 1, 2011MIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.87261
20.91731
ReflectionResolution: 1.9→65.22 Å / Num. obs: 23026 / % possible obs: 100 % / Observed criterion σ(I): 3.7 / Redundancy: 14.2 % / Biso Wilson estimate: 26.22 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→65.22 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9308 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1176 5.13 %RANDOM
Rwork0.1939 ---
obs0.196 22942 99.97 %-
Displacement parametersBiso mean: 31.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.6438 Å20 Å20 Å2
2--1.6438 Å20 Å2
3----3.2877 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.9→65.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 14 238 1892
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011728HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982347HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d549SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1728HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion15.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
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_contact2111SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2695 129 4.73 %
Rwork0.2315 2600 -
all0.2333 2729 -
obs--99.97 %

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