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- PDB-6e6a: Triclinic crystal form of IncA G144A point mutant -

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Basic information

Entry
Database: PDB / ID: 6e6a
TitleTriclinic crystal form of IncA G144A point mutant
ComponentsInclusion membrane protein A
KeywordsPROTEIN BINDING / membrane fusion / chlamydia / SNARE-like protein / inclusion
Function / homologypathogen-containing vacuole membrane / host cell membrane / extracellular region / membrane / Inclusion membrane protein A / Inclusion membrane protein A
Function and homology information
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCingolani, G. / Paumet, F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA56036 United States
National Institutes of Health/Office of the DirectorS10 OD017987 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI073486 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI116983 United States
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for the homotypic fusion of chlamydial inclusions by the SNARE-like protein IncA.
Authors: Cingolani, G. / McCauley, M. / Lobley, A. / Bryer, A.J. / Wesolowski, J. / Greco, D.L. / Lokareddy, R.K. / Ronzone, E. / Perilla, J.R. / Paumet, F.
History
DepositionJul 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Inclusion membrane protein A
A: Inclusion membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2164
Polymers39,1702
Non-polymers462
Water5,999333
1
B: Inclusion membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6313
Polymers19,5851
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inclusion membrane protein A


Theoretical massNumber of molelcules
Total (without water)19,5851
Polymers19,5851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.022, 43.533, 45.783
Angle α, β, γ (deg.)92.93, 95.96, 93.91
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Inclusion membrane protein A


Mass: 19585.117 Da / Num. of mol.: 2 / Fragment: soluble domain (UNP residues 87-246) / Mutation: G144A,V211A,V212A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: incA / Production host: Escherichia coli (E. coli) / References: UniProt: Q50FQ0, UniProt: P0CI27*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium acetate trihydrate, pH 8.0, 20% w/v PEG3350
PH range: 6.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→15 Å / Num. obs: 20042 / % possible obs: 88.1 % / Redundancy: 1.5 % / Biso Wilson estimate: 13.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 20.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 5.8 / Num. unique obs: 1478 / Rsym value: 0.131 / % possible all: 66.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E7E

6e7e


Resolution: 1.95→14.96 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.213 688 4.94 %RANDOM
Rwork0.17 ---
obs0.172 20013 87.7 %-
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 2 333 2979
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection% reflection
Rfree0.2291 73 -
Rwork0.2005 1347 -
obs-1420 66.1 %
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)
10.0699-0.03560.03140.0151-0.00820.0111-0.10520.0076-0.0233-0.1038-0.0823-0.18470.10180.1052-0.05690.14510.06660.07550.2016-0.01740.2533-19.20161.978714.9521
20.1257-0.05340.22730.14560.19130.35090.01810.0386-0.0375-0.0721-0.0229-0.005-0.03910.0166-0.00030.04320.00270.02410.05310.00730.0768-37.29749.783717.2853
30.20940.1174-0.01750.28950.11090.26620.0523-0.0772-0.1241-0.14440.08780.0859-0.08330.0140.12920.01240.0069-0.02960.0657-0.00670.0822-39.10981.787914.6945
40.2748-0.1524-0.16050.50890.01820.2147-0.0979-0.256-0.02090.06280.04450.2179-0.0550.1842-0.13010.0943-0.01460.02870.15470.01130.0251-45.971215.112942.4271
50.51450.1873-0.03440.2707-0.0010.8139-0.0839-0.10880.0249-0.0878-0.16350.1733-0.0407-0.3959-0.72370.0624-0.04250.04080.05330.0242-0.0089-49.01317.551833.985
60.220.0409-0.01070.22780.08850.19420.0326-0.10720.09970.0602-0.0449-0.0784-0.14080.1168-0.0580.131-0.0123-0.00470.0455-0.02960.0605-42.615323.561637.4777

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