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- PDB-2qdf: Structure of N-terminal domain of E. Coli YaeT -

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Basic information

Entry
Database: PDB / ID: 2qdf
TitleStructure of N-terminal domain of E. Coli YaeT
ComponentsOuter membrane protein assembly factor yaeT
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / POTRA domain
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / membrane
Similarity search - Function
membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) ...membrane protein fhac / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, S. / Malinverni, J.C. / Sliz, P. / Silhavy, T.J. / Harrison, S.C. / Kahne, D.
CitationJournal: Science / Year: 2007
Title: Structure and function of an essential component of the outer membrane protein assembly machine.
Authors: Kim, S. / Malinverni, J.C. / Sliz, P. / Silhavy, T.J. / Harrison, S.C. / Kahne, D.
History
DepositionJun 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor yaeT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4792
Polymers37,4551
Non-polymers241
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.650, 107.560, 44.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-619-

HOH

DetailsThe second molecule in the dimer is generated by the operation: -x+1, -y+1, z

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Components

#1: Protein Outer membrane protein assembly factor yaeT / Omp85


Mass: 37455.168 Da / Num. of mol.: 1 / Fragment: residues 21-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: yaeT / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A940
#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.: 119 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 10% PEG 10K, 100mM sodium acetate, 100 mM magnesium formate, 10%glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 17931 / Num. obs: 16997 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Χ2: 1.069 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1393 / Χ2: 0.971 / % possible all: 80.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å43.01 Å
Translation3.5 Å43.01 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chain A of PDB entry 2QCZ

2qcz


Resolution: 2.2→50 Å / FOM work R set: 0.769 / Cross valid method: free R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 826 4.6 %random
Rwork0.238 ---
all0.274 18007 --
obs-16932 94 %-
Solvent computationBsol: 41.299 Å2
Displacement parametersBiso mean: 50.83 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å20 Å20 Å2
2--14.354 Å20 Å2
3----19.804 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 1 119 2612
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6251.5
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_mcangle_it2.5672
X-RAY DIFFRACTIONc_scangle_it3.3422.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.2-2.250.335380.312773811
2.25-2.30.403380.317844882
2.3-2.360.334430.286917960
2.36-2.420.277490.317934983
2.42-2.490.38490.3289871036
2.49-2.570.353500.2799971047
2.57-2.670.291410.3079971038
2.67-2.770.363580.28210191077
2.77-2.90.324570.30110561113
2.9-3.050.341540.26110351089
3.05-3.240.237570.22510721129
3.24-3.490.303560.21410691125
3.49-3.840.274550.24110741129
3.84-4.40.285600.20710861146
4.4-5.540.239560.19811051161
5.54-500.269650.23211411206
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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