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- PDB-2ynq: Crystal Structure of Geobacillus thermodenitrificans EssB extrace... -

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Basic information

Entry
Database: PDB / ID: 2ynq
TitleCrystal Structure of Geobacillus thermodenitrificans EssB extracellular fragment
ComponentsESSB
KeywordsMEMBRANE PROTEIN / SECRETION / ESS / TYPE V / SECRETION SYSTEM
Function / homology
Function and homology information


identical protein binding / membrane
Similarity search - Function
Type VII secretion system EssB, C-terminal-like domain / Type VII secretion system EssB / Type VII secretion system EssB, C-terminal / WXG100 protein secretion system (Wss), protein YukC / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / Type VII secretion protein EssB
Similarity search - Component
Biological speciesGEOBACILLUS THERMODENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZoltner, M. / Fyfe, P.K. / Hunter, W.N.
CitationJournal: Structure / Year: 2013
Title: The Architecture of Essb, an Integral Membrane Component of the Type Vii Secretion System.
Authors: Zoltner, M. / Norman, D.G. / Fyfe, P.K. / El Mkami, H. / Palmer, T. / Hunter, W.N.
History
DepositionOct 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESSB
B: ESSB
C: ESSB
D: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,59116
Polymers75,9714
Non-polymers62012
Water4,432246
1
A: ESSB
D: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2848
Polymers37,9852
Non-polymers2996
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-48.7 kcal/mol
Surface area16460 Å2
MethodPISA
2
B: ESSB
hetero molecules

B: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3068
Polymers37,9852
Non-polymers3216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3830 Å2
ΔGint-53.4 kcal/mol
Surface area16590 Å2
MethodPISA
3
C: ESSB
hetero molecules

C: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3068
Polymers37,9852
Non-polymers3216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1870 Å2
ΔGint-35 kcal/mol
Surface area17910 Å2
MethodPISA
4
A: ESSB
hetero molecules

B: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3299
Polymers37,9852
Non-polymers3447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
Buried area2690 Å2
ΔGint-38.9 kcal/mol
Surface area17650 Å2
MethodPISA
5
D: ESSB
hetero molecules

C: ESSB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2617
Polymers37,9852
Non-polymers2765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2110 Å2
ΔGint-45 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.890, 110.620, 97.410
Angle α, β, γ (deg.)90.00, 103.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1392-

CL

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ESSB


Mass: 18992.742 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 241-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS THERMODENITRIFICANS (bacteria)
Strain: NG80-2 / Description: SYNTHETIC GENE / Plasmid: PET27 (MODIFIED) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A4IKE6

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Non-polymers , 5 types, 258 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 4.56 Å3/Da / Density % sol: 72.84 % / Description: NONE
Crystal growpH: 7 / Details: 3 M MALONATE PH7.0, 10 MM ZNCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2010 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→29.46 Å / Num. obs: 52114 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→94.782 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 11.965 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.204 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2215 2642 5.12 %
Rwork0.1862 --
obs0.188 52094 97.145 %
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 60.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.188 Å20 Å2-1.366 Å2
2---0.335 Å20 Å2
3----0.108 Å2
Refinement stepCycle: LAST / Resolution: 2.4→94.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 35 246 5281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9847129
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7685627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.31125.967300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.875151039
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024044
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.22471
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23632
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.53099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13425045
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84232177
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1134.52084
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: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 203 -
Rwork0.294 3649 -
obs--97.248 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.86830.62571.11112.0739-0.16633.91960.0457-0.37980.23470.3156-0.20010.3431-0.1078-0.38670.15440.1663-0.11040.01140.1453-0.03870.186520.36240.241847.5808
22.02971.46341.52691.99680.87721.60250.0315-0.19070.28780.0194-0.14850.3763-0.0705-0.17930.1170.15890.0015-0.02010.1058-0.01790.18048.9498-6.908131.6068
37.5131-2.3876-1.37523.0778.961527.63150.34780.35330.2259-0.41110.1253-0.2617-1.09640.5665-0.47310.3048-0.121-0.00970.0872-0.06060.356111.6514-12.824710.9636
42.1613-0.2530.58671.0089-0.09551.4136-0.03420.146-0.0424-0.07560.0044-0.0640.10350.07630.02980.1590.0229-0.00160.0909-0.0060.1052.9648-46.591941.9279
54.4982-4.84680.080927.65045.50175.63520.24070.40251.3043-0.365-0.29731.3896-1.0365-1.03440.05670.23040.24430.18970.28460.27720.7827-19.5591-35.627535.6716
621.055711.5002-0.42380.4717-0.6504-2.0683-1.79863.46540.1054-0.39291.87670.4560.3219-0.1-0.07811.2391-0.2327-0.15420.62090.30460.7235-21.4969-59.645333.7993
72.57310.24930.31531.73010.05722.46810.04030.019-0.0150.00050.004-0.2069-0.02230.3018-0.04430.08980.0129-0.01560.11820.00690.085311.9689-27.4944-5.1558
82.1535-0.12372.85193.0129-3.72687.97230.05410.0499-0.4692-0.34960.084-0.3370.54830.1573-0.1380.12320.08530.02110.325-0.02940.215424.4762-28.971814.4468
94.1594-2.1281-6.99431.0654.7288.62780.4894-0.06890.8253-0.62770.52-0.1788-1.28050.4378-1.00940.6597-0.3568-0.52890.50270.08560.821124.209-8.684212.8525
102.3853-0.15361.05760.89350.1341.82250.02290.0571-0.028-0.0236-0.0139-0.09610.06110.0038-0.0090.16610.0005-0.02710.13490.00050.13487.652-28.799326.7726
119.6128-1.379-6.60850.9252-0.521221.75080.29-1.6131-0.03590.8411-0.09890.099-0.95050.8096-0.19110.8982-0.38430.01270.4349-0.10210.154922.1483-25.075247.0892
1225.741512.9058-19.39328.2276-14.307122.83820.12011.0849-0.84190.1749-0.5231-0.3621-0.58271.25540.4030.182-0.20170.11630.5993-0.12310.439234.9033-22.28526.2221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A242 - 291
2X-RAY DIFFRACTION2A292 - 376
3X-RAY DIFFRACTION3A377 - 390
4X-RAY DIFFRACTION4B-1 - 348
5X-RAY DIFFRACTION5B349 - 373
6X-RAY DIFFRACTION6B374 - 389
7X-RAY DIFFRACTION7C241 - 340
8X-RAY DIFFRACTION8C341 - 370
9X-RAY DIFFRACTION9C371 - 389
10X-RAY DIFFRACTION10D0 - 348
11X-RAY DIFFRACTION11D349 - 375
12X-RAY DIFFRACTION12D376 - 390

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