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- PDB-3ec6: Crystal structure of the General Stress Protein 26 from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3ec6
TitleCrystal structure of the General Stress Protein 26 from Bacillus anthracis str. Sterne
ComponentsGeneral stress protein 26
KeywordsStructural Genomics / Unknown Function / alpha-beta structure / structural genomics of NIAID / Structural Genomics of National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase like / : / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / General stress protein 26 / General stress protein 26
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsKim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of the general stress protein 26 from Bacillus anthracis str. Sterne
Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Anderson, W.F. / Joachimiak, A.
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1703
Polymers16,2881
Non-polymers8822
Water1,58588
1
A: General stress protein 26
hetero molecules

A: General stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3396
Polymers32,5762
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2230 Å2
ΔGint-14 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.123, 48.898, 51.066
Angle α, β, γ (deg.)90.00, 126.05, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-175-

HOH

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Components

#1: Protein General stress protein 26


Mass: 16288.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q81Z55, UniProt: A0A6L8PEJ3*PLUS
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CODE IDP01540 DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING.

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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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 0.1M Hampton PH9.2, 2.8M NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→41.27 Å / Num. all: 16512 / Num. obs: 16512 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 16.02 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.5 / Num. unique all: 608 / % possible all: 71.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→26.32 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.78 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.108
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.227 840 5.1 %RANDOM
Rwork0.186 ---
all0.188 15664 --
obs0.188 15664 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.335 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.09 Å2
2--0.23 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 58 88 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8422.0151715
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1945146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57324.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.292159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021951
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11221163
X-RAY DIFFRACTIONr_scbond_it2.9343546
X-RAY DIFFRACTIONr_scangle_it4.5884.5552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 46 -
Rwork0.287 856 -
obs-902 70.69 %
Refinement TLS params.Method: refined / Origin x: -3.2248 Å / Origin y: 36.7979 Å / Origin z: 20.3917 Å
111213212223313233
T0.0193 Å20.0014 Å2-0.0085 Å2-0.0204 Å20.0076 Å2--0.0206 Å2
L0.5611 °2-0.023 °2-0.476 °2-0.4869 °20.2164 °2--1.1142 °2
S0.0466 Å °-0.0182 Å °-0.0296 Å °0.0124 Å °-0.0355 Å °-0.0315 Å °0.0531 Å °0.0582 Å °-0.0111 Å °

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