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- PDB-5fv0: The cytoplasmic domain of EssC -

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Basic information

Entry
Database: PDB / ID: 5fv0
TitleThe cytoplasmic domain of EssC
ComponentsESX secretion system protein EccC
KeywordsSECRETION / ESX-1 / P-LOOP CONTAINING DOMAIN / FTSK/SPOIIIE / PROTEIN SECRETION / ATPASE / TYPE VII
Function / homology
Function and homology information


ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane
Similarity search - Function
Firmicutes EssC, N-terminal / Firmicutes EssC, C-terminal / DNA transporter / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-ONA / ESX secretion system protein EccC
Similarity search - Component
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.91 Å
AuthorsZoltner, M. / Ng, W.M.A.V. / Palmer, T. / Hunter, W.N.
CitationJournal: Biochem. J. / Year: 2016
Title: EssC: domain structures inform on the elusive translocation channel in the Type VII secretion system.
Authors: Zoltner, M. / Ng, W.M. / Money, J.J. / Fyfe, P.K. / Kneuper, H. / Palmer, T. / Hunter, W.N.
History
DepositionFeb 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Nov 28, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3May 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ESX secretion system protein EccC
B: ESX secretion system protein EccC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1585
Polymers117,7732
Non-polymers1,3863
Water91951
1
A: ESX secretion system protein EccC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7653
Polymers58,8861
Non-polymers8792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ESX secretion system protein EccC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3942
Polymers58,8861
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.917, 152.372, 207.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9388, -0.16, -0.305), (-0.1604, -0.9868, 0.02388), (-0.3048, 0.02651, -0.952)
Vector: 175.542, 162.184, 4.97051)

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Components

#1: Protein ESX secretion system protein EccC / Type VII secretion system protein EccC / T7SS protein EccC


Mass: 58886.328 Da / Num. of mol.: 2 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 966-1479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Gene: eccC, essC, GTNG_0419 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A4IKE7
#2: Chemical ChemComp-ONA / 3'-O-[2-(METHYLAMINO)BENZOYL]ADENOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) / 2'(3')-O-(N-METHYLANTHRANILOYL)-ADENOSINE 5'-TRIPHOSPHATE


Mass: 640.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N6O14P3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.95 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growDetails: 0.1M SODIUM CACODYLATE PH 6.2, 0.2M CALCIUM ACETATE, 20% (W/V) PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 15, 2011 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.91→29.63 Å / Num. obs: 29986 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 12.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.8
Reflection shellResolution: 2.91→3.07 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 4 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.91→122.75 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.892 / SU B: 43.416 / SU ML: 0.385 / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27484 1514 5 %RANDOM
Rwork0.26133 ---
obs0.26202 28472 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.276 Å2
Baniso -1Baniso -2Baniso -3
1-5.47 Å20 Å20 Å2
2---1.26 Å20 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.91→122.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7741 0 88 51 7880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0198034
X-RAY DIFFRACTIONr_bond_other_d0.0010.027759
X-RAY DIFFRACTIONr_angle_refined_deg0.7321.98710867
X-RAY DIFFRACTIONr_angle_other_deg0.619317870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6915960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.85524.538379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.079151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1791548
X-RAY DIFFRACTIONr_chiral_restr0.0410.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218942
X-RAY DIFFRACTIONr_gen_planes_other00.021805
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_it0.3264.6233870
X-RAY DIFFRACTIONr_mcbond_other0.3264.6233869
X-RAY DIFFRACTIONr_mcangle_it0.6246.9234820
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.1394.6884164
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: 2.91→2.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 76 -
Rwork0.389 1877 -
obs--87.74 %
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)
12.9678-0.26010.85742.1077-1.20882.03510.05310.042-0.22080.14090.09370.06680.0347-0.3034-0.14680.0633-0.00250.02480.17520.02810.263747.81140.97742.215
20.9410.2511-1.1720.2533-0.2851.48990.0326-0.0571-0.00590.11270.0205-0.2798-0.06430.1283-0.05310.11820.0085-0.12490.1986-0.06120.428661.15342.56139.174
31.7407-0.91351.87171.0764-0.33663.93230.025-0.2626-0.23260.22290.05930.05980.0071-0.6953-0.08430.16890.0056-0.06850.23180.07950.257239.94137.34144.61
40.52950.1975-0.14794.6149-0.58931.5644-0.16490.00080.02750.12010.02530.19080.12010.07620.13960.1176-0.02140.01840.14470.08870.256259.52810.32682.68
510.27650.6057-0.39745.6773-1.64711.8378-0.09320.18481.0918-0.55460.30270.1831-0.2090.3151-0.20950.2171-0.1353-0.02320.19740.05010.236663.03526.50475.061
61.7609-0.4612-0.12922.3132-1.33242.9641-0.05630.01530.16490.0335-0.1216-0.061-0.3847-0.03870.17790.2253-0.0614-0.11370.05650.05680.252560.91539.416111.092
70.9076-0.61431.48350.4233-1.01232.4401-0.01720.37140.1655-0.0231-0.2435-0.12980.02250.61350.26070.1607-0.0698-0.02660.30360.06690.38270.85532.014113.72
80.3051-0.9139-0.4954.01670.25813.4696-0.06080.0454-0.02060.19790.03030.3035-0.7757-0.54060.03040.43480.1441-0.14790.10150.01690.182950.36843.039110.69
91.55310.60250.31686.2022-1.69432.2247-0.06020.10620.12930.38090.16510.6468-0.32760.0845-0.10490.14610.00120.01760.04280.06220.332857.23768.34972.11
102.64620.1237-0.59095.4406-1.31093.17460.04330.1799-0.0054-0.36040.1286-0.41670.04770.3733-0.17190.0588-0.01890.04790.14990.04180.278166.74462.72466.956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A968 - 1065
2X-RAY DIFFRACTION2A1066 - 1188
3X-RAY DIFFRACTION3A1189 - 1240
4X-RAY DIFFRACTION4A1241 - 1452
5X-RAY DIFFRACTION5A1453 - 1479
6X-RAY DIFFRACTION6B968 - 1079
7X-RAY DIFFRACTION7B1080 - 1189
8X-RAY DIFFRACTION8B1190 - 1239
9X-RAY DIFFRACTION9B1240 - 1364
10X-RAY DIFFRACTION10B1365 - 1479

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