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- PDB-4e9j: Crystal structure of the N-terminal domain of the secretin XcpQ f... -

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Basic information

Entry
Database: PDB / ID: 4e9j
TitleCrystal structure of the N-terminal domain of the secretin XcpQ from Pseudomonas aeruginosa
ComponentsGeneral secretion pathway protein D
KeywordsPROTEIN TRANSPORT / Homodimer / XcpQ / periplasmic domain / Structural Protein / Periplasmic space / outer membrane
Function / homology
Function and homology information


protein secretion by the type II secretion system / type II protein secretion system complex / protein secretion / cell outer membrane / identical protein binding
Similarity search - Function
: / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily ...: / GspD-like, N0 domain / Ribosomal Protein S8; Chain: A, domain 1 - #120 / Type II secretion system protein GspD / GspD/PilQ family / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsVan der Meeren, R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: New Insights into the Assembly of Bacterial Secretins: STRUCTURAL STUDIES OF THE PERIPLASMIC DOMAIN OF XcpQ FROM PSEUDOMONAS AERUGINOSA.
Authors: Van der Meeren, R. / Wen, Y. / Van Gelder, P. / Tommassen, J. / Devreese, B. / Savvides, S.N.
History
DepositionMar 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Feb 6, 2013Group: Database references
Revision 1.4Feb 28, 2024Group: 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_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: General secretion pathway protein D
B: General secretion pathway protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0643
Polymers53,0402
Non-polymers241
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: General secretion pathway protein D


Theoretical massNumber of molelcules
Total (without water)26,5201
Polymers26,5201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: General secretion pathway protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5442
Polymers26,5201
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.500, 39.720, 93.300
Angle α, β, γ (deg.)90.00, 99.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

MG

21A-377-

HOH

31B-457-

HOH

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Components

#1: Protein General secretion pathway protein D


Mass: 26519.895 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 35-277
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692/PAO1/1C/PRS 101/LMG 12228 / Gene: xcpQ, PA3105 / Production host: Escherichia coli (E. coli) / References: UniProt: P35818
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris pH 8.5, 25% PEG3350, EVAPORATION, temperature 293.15K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9193 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9193 Å / Relative weight: 1
ReflectionResolution: 2.03→39.67 Å / Num. obs: 28407 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 32.42 Å2

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Processing

Software
NameVersionClassification
Proxima1 Soleildata collection
PHASERphasing
PHENIX+ BUSTER 2.10.0refinement
XDSdata reduction
autoPROCdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.03→45.96 Å / Cor.coef. Fo:Fc: 0.9175 / Cor.coef. Fo:Fc free: 0.8991 / SU R Cruickshank DPI: 0.492 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1382 4.96 %RANDOM
Rwork0.2104 ---
obs0.2123 27839 98.29 %-
all-28407 --
Displacement parametersBiso mean: 36.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.6839 Å20 Å21.304 Å2
2---1.6624 Å20 Å2
3----1.0215 Å2
Refine analyzeLuzzati coordinate error obs: 0.262 Å
Refinement stepCycle: LAST / Resolution: 2.03→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 1 203 3304
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONf_bond_d0.016175HARMONIC2
X-RAY DIFFRACTIONf_angle_deg1.1611170HARMONIC2
X-RAY DIFFRACTIONf_dihedral_angle_d1339SINUSOIDAL2
X-RAY DIFFRACTIONf_incorr_chiral_ct
X-RAY DIFFRACTIONf_pseud_angle
X-RAY DIFFRACTIONf_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONf_gen_planes954HARMONIC5
X-RAY DIFFRACTIONf_it6175HARMONIC20
X-RAY DIFFRACTIONf_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONf_omega_torsion3.58
X-RAY DIFFRACTIONf_other_torsion14.51
X-RAY DIFFRACTIONf_improper_torsion
X-RAY DIFFRACTIONf_chiral_improper_torsion455SEMIHARMONIC5
X-RAY DIFFRACTIONf_sum_occupancies
X-RAY DIFFRACTIONf_utility_distance
X-RAY DIFFRACTIONf_utility_angle
X-RAY DIFFRACTIONf_utility_torsion
X-RAY DIFFRACTIONf_ideal_dist_contact6824SEMIHARMONIC4
LS refinement shellResolution: 2.03→2.11 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2329 144 4.94 %
Rwork0.2077 2772 -
all0.2089 2916 -
obs--98.29 %

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