[English] 日本語
Yorodumi
- PDB-3g9k: Crystal structure of Bacillus anthracis transpeptidase enzyme CapD -

+
Open data


ID or keywords:

Loading...

-
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
Revision 1.7Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more