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- PDB-6top: Structure of the PorE C-terminal domain, a protein of T9SS from P... -

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Basic information

Entry
Database: PDB / ID: 6top
TitleStructure of the PorE C-terminal domain, a protein of T9SS from Porphyromonas gingivalis
Components(OmpA family protein) x 2
KeywordsPROTEIN BINDING / Peptidoglycan binding protein Type IX secretion system Porphyromonas gingivalis
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
WD40-like beta propeller / WD40-like Beta Propeller Repeat / Outer membrane protein, bacterial / Carboxypeptidase-like, regulatory domain superfamily / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Six-bladed beta-propeller, TolB-like ...WD40-like beta propeller / WD40-like Beta Propeller Repeat / Outer membrane protein, bacterial / Carboxypeptidase-like, regulatory domain superfamily / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Six-bladed beta-propeller, TolB-like / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-MLD / OmpA family protein
Similarity search - Component
Biological speciesPorphyromonas gingivalis JCVI SC001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsTrinh, T.N. / Cambillau, C. / Roussel, A. / Leone, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0019-01 France
CitationJournal: Sci Rep / Year: 2020
Title: Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment.
Authors: Trinh, N.T.T. / Tran, H.Q. / Van Dong, Q. / Cambillau, C. / Roussel, A. / Leone, P.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionJun 17, 2020ID: 6I9O
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpA family protein
B: OmpA family protein
C: OmpA family protein
D: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,53212
Polymers68,7534
Non-polymers3,7808
Water13,583754
1
A: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5483
Polymers17,6031
Non-polymers9452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9953
Polymers17,0501
Non-polymers9452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9953
Polymers17,0501
Non-polymers9452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: OmpA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9953
Polymers17,0501
Non-polymers9452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.030, 52.220, 66.560
Angle α, β, γ (deg.)90.00, 108.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OmpA family protein


Mass: 17602.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis JCVI SC001 (bacteria)
Gene: A343_1565 / Production host: Escherichia coli (E. coli) / References: UniProt: T2NEY1
#2: Protein OmpA family protein


Mass: 17050.070 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis JCVI SC001 (bacteria)
Gene: A343_1565 / Production host: Escherichia coli (E. coli) / References: UniProt: T2NEY1
#3: Chemical
ChemComp-MLD / GLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA / 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE


Mass: 921.899 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H59N7O20 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.38 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M sodium acetate 0.1M MES 30% (w/v) PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.55→49.35 Å / Num. obs: 96340 / % possible obs: 97.6 % / Redundancy: 22 % / Biso Wilson estimate: 29.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Rrim(I) all: 0.09 / Net I/σ(I): 19.7
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 14 % / Num. unique obs: 5637 / CC1/2: 0.85 / % possible all: 77.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.088 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.082
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 4772 4.96 %RANDOM
Rwork0.1899 ---
obs0.1911 96279 97.6 %-
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8087 Å20 Å2-0.5618 Å2
2--1.4898 Å20 Å2
3----0.6811 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.55→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4812 0 125 756 5693
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085022HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956784HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1853SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes876HARMONIC5
X-RAY DIFFRACTIONt_it5022HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion13.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion661SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5363SEMIHARMONIC4
LS refinement shellResolution: 1.55→2 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3276 113 5.87 %
Rwork0.32 1813 -
all0.3205 1926 -
obs--73.14 %
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)
11.3740.5312-00.9283-0.02621.4759-0.1110.2451-0.1575-0.07470.1559-0.06030.0698-0.0163-0.0449-0.0843-0.04080.01960.0485-0.0305-0.070566.231-7.4856-8.8948
21.50530.44370.45211.10070.04891.965-0.0687-0.08530.19870.0122-0.06070.1266-0.1736-0.29390.1295-0.09020.0492-0.01810.0154-0.0228-0.05761.472611.832315.1289
31.91990.5008-0.16881.38690.23932.3117-0.18920.435-0.2282-0.11010.1834-0.2305-0.02060.39130.0058-0.1499-0.07870.04170.0946-0.065-0.077789.2134-2.9776-7.9581
41.6320.28160.55990.87650.57361.8908-0.06960.05350.08760.0199-0.0035-0.0538-0.13220.0180.0731-0.04140.0042-0.0428-0.10280.02-0.023484.165912.818119.046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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