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- PDB-3ga9: Crystal structure of Bacillus anthracis transpeptidase enzyme Cap... -

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Basic information

Entry
Database: PDB / ID: 3ga9
TitleCrystal structure of Bacillus anthracis transpeptidase enzyme CapD, crystal form II
Components(Capsule biosynthesis protein capD) x 2
KeywordsHYDROLASE / CapD protein / Bacillus anthracis / The Great Lakes Regional Center of Excellence / GLRCE / Capsule biogenesis/degradation / Virulence
Function / homology
Function and homology information


capsule polysaccharide biosynthetic process / Transferases; Acyltransferases; Aminoacyltransferases / peptidase activity / transferase activity / proteolysis
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #230 / Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Capsule biosynthesis protein CapD proenzyme
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, R. / Wu, R. / Richter, S. / Anderson, V.J. / Missiakas, D. / Joachimiak, A.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of Bacillus anthracis Transpeptidase Enzyme CapD.
Authors: Wu, R. / Richter, S. / Zhang, R.G. / Anderson, V.J. / Missiakas, D. / Joachimiak, A.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 19, 2011Group: Structure summary
Revision 1.3Nov 2, 2011Group: Structure summary
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Capsule biosynthesis protein capD
S: Capsule biosynthesis protein capD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1124
Polymers55,8182
Non-polymers2942
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-54.9 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.704, 72.000, 128.853
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 Capsule biosynthesis protein capD


Mass: 36223.242 Da / Num. of mol.: 1 / Fragment: UNP residues 29-351
Source method: isolated from a genetically manipulated source
Details: Large chain / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A0389
Gene: BAK_B0097, BXB0063, capD, dep, GBAA_pXO2_0063, pXO2-55
Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51693
#2: Protein Capsule biosynthesis protein capD


Mass: 19594.777 Da / Num. of mol.: 1 / Fragment: UNP residues 352-528
Source method: isolated from a genetically manipulated source
Details: Small chain / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A0389 / Gene: capD, dep, pXO2-55, BXB0063, GBAA_pXO2_0063 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51693
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 12.5% PEGS 3350, 0.1M LiSO4, 0.1M Na Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2006 / Details: mirror
RadiationMonochromator: Si(111) channel / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. all: 23226 / Num. obs: 22962 / % possible obs: 98 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 20.4
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 1.92 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.43 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.257
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 1022 5.1 %RANDOM
Rwork0.19717 ---
obs0.20002 19203 99.08 %-
all-19203 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.379 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.72 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3507 0 19 79 3605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223594
X-RAY DIFFRACTIONr_bond_other_d0.0010.022500
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9784837
X-RAY DIFFRACTIONr_angle_other_deg1.06136121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3545450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34924.57151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57615655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6931517
X-RAY DIFFRACTIONr_chiral_restr0.2180.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023961
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
X-RAY DIFFRACTIONr_nbd_refined0.210.2869
X-RAY DIFFRACTIONr_nbd_other0.1920.22571
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21748
X-RAY DIFFRACTIONr_nbtor_other0.0880.21894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.831.52900
X-RAY DIFFRACTIONr_mcbond_other0.1131.5937
X-RAY DIFFRACTIONr_mcangle_it1.01623610
X-RAY DIFFRACTIONr_scbond_it1.58331595
X-RAY DIFFRACTIONr_scangle_it2.3544.51227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 70 -
Rwork0.236 1373 -
obs--98.43 %
Refinement TLS params.Method: refined / Origin x: 8.631 Å / Origin y: 67.469 Å / Origin z: 18.638 Å
111213212223313233
T-0.2353 Å2-0.008 Å2-0.0319 Å2--0.3767 Å20.0905 Å2---0.3448 Å2
L2.564 °20.3042 °2-0.1998 °2-1.9209 °2-0.6331 °2--2.5883 °2
S-0.1726 Å °0.3699 Å °0.2525 Å °-0.0741 Å °0.015 Å °-0.0655 Å °-0.0265 Å °0.0917 Å °0.1577 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L46 - 119
2X-RAY DIFFRACTION1L120 - 193
3X-RAY DIFFRACTION1L194 - 282
4X-RAY DIFFRACTION1L283 - 335
5X-RAY DIFFRACTION1S352 - 417
6X-RAY DIFFRACTION1S420 - 460
7X-RAY DIFFRACTION1S461 - 527

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