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- PDB-3bs6: 1.8 Angstrom crystal structure of the periplasmic domain of the m... -

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Basic information

Entry
Database: PDB / ID: 3bs6
Title1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC
ComponentsInner membrane protein oxaA
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / YIDC/OXA1/ALB3 family / Membrane insertion / Chaperone / SEC translocon / Periplasmic domain / Beta supersandwich fold / Helical linker domain
Function / homology
Function and homology information


: / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein folding / protein-containing complex assembly / membrane / plasma membrane
Similarity search - Function
Beta-galactosidase; Chain A, domain 5 - #90 / Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18 / Beta-galactosidase; Chain A, domain 5 ...Beta-galactosidase; Chain A, domain 5 - #90 / Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / Membrane insertase YidC / : / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsRavaud, S. / Sinning, I.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of the Periplasmic Domain of the Escherichia coli Membrane Protein Insertase YidC Contains a Substrate Binding Cleft
Authors: Ravaud, S. / Stjepanovic, G. / Wild, K. / Sinning, I.
History
DepositionDec 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_label_seq_id / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: Inner membrane protein oxaA
B: Inner membrane protein oxaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,44919
Polymers61,7552
Non-polymers1,69417
Water8,071448
1
A: Inner membrane protein oxaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,75912
Polymers30,8781
Non-polymers88111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inner membrane protein oxaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6907
Polymers30,8781
Non-polymers8136
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Inner membrane protein oxaA
hetero molecules

A: Inner membrane protein oxaA
hetero molecules

B: Inner membrane protein oxaA
hetero molecules

B: Inner membrane protein oxaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,89838
Polymers123,5104
Non-polymers3,38834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_657-x+1,y,-z+21
Buried area10150 Å2
ΔGint-74.5 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.150, 55.640, 63.330
Angle α, β, γ (deg.)90.000, 101.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-591-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inner membrane protein oxaA / Periplasmic domain of YidC (P1D)


Mass: 30877.549 Da / Num. of mol.: 2 / Fragment: UNP residues 56-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: oxaA, yidC / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: P25714

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Non-polymers , 6 types, 465 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 21% PEG3350, 0.2M calcium acetate, 10% ethylene glycol, VAPOR DIFFUSION, pH7.5, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→44.99 Å / Num. obs: 49763 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.428 / % possible all: 96.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0008refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→38.9 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.533 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1994 4 %RANDOM
Rwork0.178 ---
obs0.179 49625 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 104 448 4564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224198
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.975694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44626.114193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43715641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1111510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2622
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023214
X-RAY DIFFRACTIONr_nbd_refined0.2080.21883
X-RAY DIFFRACTIONr_nbtor_refined0.3080.22770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2429
X-RAY DIFFRACTIONr_metal_ion_refined0.080.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.231
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1050.25
X-RAY DIFFRACTIONr_mcbond_it1.78722664
X-RAY DIFFRACTIONr_mcangle_it2.52334195
X-RAY DIFFRACTIONr_scbond_it2.20621735
X-RAY DIFFRACTIONr_scangle_it3.09931492
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 141 -
Rwork0.27 3380 -
all-3521 -
obs--100 %

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