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- PDB-3zbh: Geobacillus thermodenitrificans EsxA crystal form I -

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Basic information

Entry
Database: PDB / ID: 3zbh
TitleGeobacillus thermodenitrificans EsxA crystal form I
ComponentsESXA
KeywordsUNKNOWN FUNCTION / TYPE 7 SECRETION / ESAT6 FAMILY PROTEINS / WXG PROTEIN ESS
Function / homology
Function and homology information


ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / ESAT-6-like protein
Similarity search - Component
Biological speciesGEOBACILLUS THERMODENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsNg, W.M. / Zoltner, M. / Palmer, T. / Hunter, W.N.
CitationJournal: To be Published
Title: Crystal Structure of the Homodimeric Esat-6-Family Proteins Esxa and Esxb from Geobacillus Thermodenitrificans
Authors: Zoltner, M. / Ng, W.M. / Palmer, T. / Hunter, W.N.
History
DepositionNov 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESXA
B: ESXA
C: ESXA
D: ESXA
E: ESXA
F: ESXA
G: ESXA
H: ESXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,85816
Polymers88,3148
Non-polymers5448
Water5,495305
1
A: ESXA
B: ESXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5058
Polymers22,0792
Non-polymers4266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-46 kcal/mol
Surface area10850 Å2
MethodPISA
2
G: ESXA
H: ESXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1383
Polymers22,0792
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-34.6 kcal/mol
Surface area11350 Å2
MethodPISA
3
C: ESXA
D: ESXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1383
Polymers22,0792
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-35.7 kcal/mol
Surface area11100 Å2
MethodPISA
4
E: ESXA
F: ESXA


Theoretical massNumber of molelcules
Total (without water)22,0792
Polymers22,0792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-38 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.948, 58.641, 85.219
Angle α, β, γ (deg.)90.00, 112.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ESXA


Mass: 11039.270 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: SYNTHETIC GENE (CODON ADAPTED) / Source: (synth.) GEOBACILLUS THERMODENITRIFICANS (bacteria) / References: UniProt: A4IKE4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.25 Å3/Da / Density % sol: 45.5 % / Description: NONE
Crystal growpH: 4.5 / Details: RESERVOIR 0.1 M NH4AC PH4.5, 1 M (NH4)2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.044
DetectorType: DECTRIS TWO-DIMENSIONAL HYBRID PIXEL ARRAY / Date: Feb 19, 2012 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 1.94→35 Å / Num. obs: 56211 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.9
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GTHESXA CRYSTAL FORM II

Resolution: 1.94→34.28 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.136 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25901 2848 5.1 %RANDOM
Rwork0.20873 ---
obs0.21131 53299 97.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.817 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.94→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5817 0 34 305 6156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9498293
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8245766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.97625.619331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.958151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1741543
X-RAY DIFFRACTIONr_chiral_restr0.080.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024737
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 200 -
Rwork0.242 3787 -
obs--96.35 %

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