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- PDB-2bb3: Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylas... -

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Basic information

Entry
Database: PDB / ID: 2bb3
TitleCrystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus
Componentscobalamin biosynthesis precorrin-6Y methylase (cbiE)
KeywordsTRANSFERASE / beta / alpha-beta-alpha sandwich / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein methyltransferase activity / cobalamin biosynthetic process
Similarity search - Function
Precorrin-6Y methyltransferase / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily ...Precorrin-6Y methyltransferase / Tetrapyrrole methylase, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Cobalamin biosynthesis precorrin-6Y methylase (CbiE)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å
AuthorsKim, Y. / Joachimiak, A. / Xu, X. / Savchenko, A. / Edwards, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus
Authors: Kim, Y. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionOct 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE AUTHORS STATE THE BIOLOGICAL UNIT COULD BE A DIMER. THE ASYMMETRIC UNIT CONTAINS TWO "HALF DIMERS".

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
B: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2664
Polymers50,4982
Non-polymers7692
Water3,243180
1
A: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
hetero molecules

A: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2664
Polymers50,4982
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3650 Å2
ΔGint-14 kcal/mol
Surface area18590 Å2
MethodPISA, PQS
2
B: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
hetero molecules

B: cobalamin biosynthesis precorrin-6Y methylase (cbiE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2664
Polymers50,4982
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3500 Å2
ΔGint-18 kcal/mol
Surface area18020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.191, 88.418, 115.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

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Components

#1: Protein cobalamin biosynthesis precorrin-6Y methylase (cbiE)


Mass: 25248.838 Da / Num. of mol.: 2 / Fragment: CbiE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: O29536, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium Acetate, 11% PEG10K, 2% Iso-Propanol,10mM SAH, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 28, 2004 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.2→44.21 Å / Num. all: 24301 / Num. obs: 22771 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 37.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 2.56 / % possible all: 82.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→29.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1862364.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1985 10.1 %RANDOM
Rwork0.211 ---
all0.2174 19665 --
obs0.211 19665 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.787 Å2 / ksol: 0.288362 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2--2.88 Å20 Å2
3----4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.27→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 52 180 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it3.582
X-RAY DIFFRACTIONc_scbond_it2.812
X-RAY DIFFRACTIONc_scangle_it4.362.5
LS refinement shellResolution: 2.27→2.41 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 260 9.9 %
Rwork0.258 2358 -
obs-2358 75.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4sah.paramsah.top

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