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- PDB-3x3m: Crystal structure of EccB1 of Mycobacterium tuberculosis in space... -

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Basic information

Entry
Database: PDB / ID: 3x3m
TitleCrystal structure of EccB1 of Mycobacterium tuberculosis in spacegroup P212121
ComponentsESX-1 secretion system protein EccB1
KeywordsPROTEIN TRANSPORT / alpha-beta-alpha sandwich / beta-sheet / ATPase
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / Hydrolases; Acting on acid anhydrides / peptidoglycan-based cell wall / hydrolase activity / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / TTHA1013/TTHA0281-like / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich ...Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 domain / TTHA1013/TTHA0281-like / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / ESX-1 secretion system ATPase EccB1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, X.L. / Li, D.F. / Zhang, X.E. / Bi, L.J. / Wang, D.C.
CitationJournal: Faseb J. / Year: 2015
Title: Core component EccB1 of the Mycobacterium tuberculosis type VII secretion system is a periplasmic ATPase.
Authors: Zhang, X.L. / Li, D.F. / Fleming, J. / Wang, L.W. / Zhou, Y. / Wang, D.C. / Zhang, X.E. / Bi, L.J.
History
DepositionJan 24, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-1 secretion system protein EccB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7853
Polymers45,7051
Non-polymers802
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.630, 108.730, 114.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ESX-1 secretion system protein EccB1 / Secretion protein EccB


Mass: 45704.742 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: LH57_21080, P425_04028, Rv3869, RVBD_3869 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6Y4Q7, UniProt: P9WNR7*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.15 Å3/Da / Density % sol: 42.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20mM Tris-Cl pH 7.5, 100mM magnesium formate, 15% [w/v] PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 3, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.42 Å / Num. all: 32078 / Num. obs: 31116 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3779 / Rsym value: 0.227 / % possible all: 84.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X3N

3x3n


Resolution: 1.9→36.021 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 20.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1993 6.42 %RANDOM
Rwork0.1843 ---
all0.1869 32078 --
obs0.1869 31051 96.54 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.978 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8093 Å2-0 Å2-0 Å2
2---3.2313 Å2-0 Å2
3---0.422 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 2 488 3450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043040
X-RAY DIFFRACTIONf_angle_d0.9364178
X-RAY DIFFRACTIONf_dihedral_angle_d12.8371111
X-RAY DIFFRACTIONf_chiral_restr0.055491
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94750.30481080.2337158675
1.9475-2.00020.26911320.1981184188
2.0002-2.0590.25331310.198204397
2.059-2.12550.25651400.1883205897
2.1255-2.20140.21121490.1794206599
2.2014-2.28960.26331330.1898211698
2.2896-2.39380.22021540.19052094100
2.3938-2.51990.25651390.1862211399
2.5199-2.67780.241480.1906212699
2.6778-2.88440.22191430.19832165100
2.8844-3.17450.24511550.18692146100
3.1745-3.63350.24391480.18132160100
3.6335-4.57640.17751530.15332215100
4.5764-36.02730.1931600.19212330100
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)
10.5722-0.5809-0.43251.47030.87171.13330.00060.0368-0.06960.029-0.02890.03590.1685-0.0218-0.00230.0557-0.0036-0.02410.06470.00610.063710.3775-16.0808-8.9933
20.27160.0107-0.00482.83271.0890.4256-0.02120.03680.03250.03790.03420.0138-0.04150.0123-0.0130.0706-0.0029-0.00060.10280.02740.06174.811821.72329.3909
31.3469-0.3465-0.28761.57620.59131.4224-0.040.0952-0.1622-0.1065-0.00890.00370.12750.04850.04070.04680.0166-0.02340.0603-0.01180.072913.6206-12.8499-9.0193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ -1:135)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 136:293)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 294:394)

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