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- PDB-3g9k: Crystal structure of Bacillus anthracis transpeptidase enzyme CapD -

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Basic information

Entry
Database: PDB / ID: 3g9k
TitleCrystal structure of Bacillus anthracis transpeptidase enzyme CapD
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 ...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 / MOLECULAR REPLACEMENT / Resolution: 1.79 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 13, 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
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
D: Capsule biosynthesis protein capD
F: Capsule biosynthesis protein capD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9306
Polymers111,6364
Non-polymers2942
Water9,998555
1
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-51.8 kcal/mol
Surface area18320 Å2
MethodPISA
2
D: Capsule biosynthesis protein capD
F: Capsule biosynthesis protein capD


Theoretical massNumber of molelcules
Total (without water)55,8182
Polymers55,8182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-50.3 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.668, 120.621, 77.375
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsule biosynthesis protein capD


Mass: 36223.242 Da / Num. of mol.: 2 / Fragment: UNP residues 29-351
Source method: isolated from a genetically manipulated source
Details: Long 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.: 2 / Fragment: UNP residues 352-528
Source method: isolated from a genetically manipulated source
Details: Short 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.: 555 / 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: 2.2 Å3/Da / Density % sol: 44.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 3350, 8% PEG 400, 0.05M 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: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. all: 88013 / Num. obs: 83551 / % possible obs: 98 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 16.1
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.73 / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GA9

3ga9


Resolution: 1.79→40.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.964 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24166 4413 5 %RANDOM
Rwork0.19653 ---
obs0.19875 83551 97.58 %-
all-83551 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.615 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20.25 Å2
2--3.42 Å20 Å2
3----2.01 Å2
Refinement stepCycle: LAST / Resolution: 1.79→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6904 0 19 555 7478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227058
X-RAY DIFFRACTIONr_bond_other_d0.0010.024923
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9779492
X-RAY DIFFRACTIONr_angle_other_deg0.968312057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.155885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5524.399291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.673151292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8861535
X-RAY DIFFRACTIONr_chiral_restr0.1010.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021370
X-RAY DIFFRACTIONr_nbd_refined0.2220.21707
X-RAY DIFFRACTIONr_nbd_other0.1940.25100
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23399
X-RAY DIFFRACTIONr_nbtor_other0.0880.23723
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2513
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2221.55362
X-RAY DIFFRACTIONr_mcbond_other0.2371.51841
X-RAY DIFFRACTIONr_mcangle_it1.54927096
X-RAY DIFFRACTIONr_scbond_it2.36733036
X-RAY DIFFRACTIONr_scangle_it3.1894.52396
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 274 -
Rwork0.261 5063 -
obs--79.99 %
Refinement TLS params.Method: refined / Origin x: 14.453 Å / Origin y: -17.479 Å / Origin z: 19.274 Å
111213212223313233
T0.0262 Å2-0.0117 Å20.0206 Å2-0.0147 Å20.0135 Å2--0.0804 Å2
L0.0633 °2-0.1116 °2-0.0084 °2-0.2437 °20.0986 °2--0.1507 °2
S-0.017 Å °-0.0119 Å °-0.0135 Å °-0.0028 Å °0.0021 Å °0.0267 Å °-0.0005 Å °0.0264 Å °0.015 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L46 - 100
2X-RAY DIFFRACTION1L101 - 150
3X-RAY DIFFRACTION1L151 - 200
4X-RAY DIFFRACTION1L201 - 260
5X-RAY DIFFRACTION1L261 - 332
6X-RAY DIFFRACTION1S1 - 2
7X-RAY DIFFRACTION1S352 - 392
8X-RAY DIFFRACTION1S403 - 460
9X-RAY DIFFRACTION1S461 - 527
10X-RAY DIFFRACTION1D46 - 98
11X-RAY DIFFRACTION1D101 - 150
12X-RAY DIFFRACTION1D151 - 200
13X-RAY DIFFRACTION1D201 - 260
14X-RAY DIFFRACTION1D261 - 334
15X-RAY DIFFRACTION1F352 - 391
16X-RAY DIFFRACTION1F403 - 450
17X-RAY DIFFRACTION1F451 - 526

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