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- PDB-7tm8: Crystal structure of Bifunctional adenosylcobalamin biosynthesis ... -

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Basic information

Entry
Database: PDB / ID: 7tm8
TitleCrystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae
ComponentsBifunctional adenosylcobalamin biosynthesis protein
KeywordsTRANSFERASE / Bifunctional adenosylcobalamin biosynthesis protein / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homology
Function and homology information


: / : / adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / GTP binding / ATP binding
Similarity search - Function
Cobinamide kinase/cobinamide phosphate guanyltransferase / Cobinamide kinase / cobinamide phosphate guanyltransferase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bifunctional adenosylcobalamin biosynthesis protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: To be published
Title: Crystal structure of Bifunctional adenosylcobalamin biosynthesis protein from Klebsiella pneumoniae
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C.
History
DepositionJan 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional adenosylcobalamin biosynthesis protein
B: Bifunctional adenosylcobalamin biosynthesis protein
C: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,06010
Polymers62,3873
Non-polymers6727
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-149 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.138, 63.279, 131.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional adenosylcobalamin biosynthesis protein


Mass: 20795.762 Da / Num. of mol.: 3 / Fragment: KlpnC.20504.a.B1 / Mutation: A75E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_42470 / Plasmid: KlpnC.20504.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GSH0, adenosylcobinamide kinase, adenosylcobinamide-phosphate guanylyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.62 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index A4: 2.0 M Ammonium sulfate, 0.1 M BIS-TRIS, KlpnC.20504.a.B1.PW39083 at 40 mg/mL, Tray: plate 12369 well A4 drop 1, Puck: PSL0616, Cryo: 80% crystallant + 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.65→65.8 Å / Num. obs: 64185 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.034 / Rrim(I) all: 0.083 / Net I/σ(I): 12.4 / Num. measured all: 381328 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.696.20.8422914846850.7470.3650.9192.399.9
7.38-65.85.10.03942968420.9990.0170.04331.799.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.32 Å45.61 Å
Translation3.32 Å45.61 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9K

1c9k


Resolution: 1.65→45.56 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 3088 4.82 %
Rwork0.1766 60988 -
obs0.1779 64076 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.55 Å2 / Biso mean: 25.8344 Å2 / Biso min: 12.96 Å2
Refinement stepCycle: final / Resolution: 1.65→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 35 512 4339
Biso mean--31.66 35.29 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.25441360.227927412877100
1.68-1.70.27361340.226627282862100
1.7-1.730.27071360.22327292865100
1.73-1.760.2721100.222127932903100
1.76-1.80.28841630.226426942857100
1.8-1.830.27781370.226827582895100
1.83-1.870.21941380.204927452883100
1.87-1.920.22641310.183927752906100
1.92-1.970.18051200.17472750287099
1.97-2.020.1671120.17672736284899
2.02-2.080.18881550.162527622917100
2.08-2.150.21071360.170727562892100
2.15-2.220.20441550.166727302885100
2.22-2.310.19641300.165827932923100
2.31-2.420.20581220.165628012923100
2.42-2.540.20611310.172427732904100
2.54-2.70.21791730.179327532926100
2.7-2.910.20441560.18142752290899
2.91-3.210.19671640.179127932957100
3.21-3.670.18821310.157628302961100
3.67-4.620.18291370.150328612998100
4.62-45.560.20471810.19392935311699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3948-0.06450.09410.72470.07160.95890.0234-0.0727-0.11660.09-0.00550.08680.1224-0.0372-0.02220.1703-0.01390.00720.13390.00270.134-20.4197-1.39783.0016
20.97530.07810.11421.06820.18151.3620.00540.05620.1088-0.0317-0.03130.124-0.0808-0.10620.03780.15180.0003-0.00180.14220.00910.1518-18.45819.4506-20.1661
31.39130.03910.11111.3362-0.00840.6868-0.01450.1635-0.0188-0.11010.0311-0.08640.05680.1248-0.02020.16850.0097-0.00710.1905-0.00330.12612.8177-3.356-18.4663
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -1 through 181)A-1 - 181
2X-RAY DIFFRACTION2(chain 'B' and resid -2 through 181)B-2 - 181
3X-RAY DIFFRACTION3(chain 'C' and resid -2 through 181)C-2 - 181

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