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- PDB-3cw0: E.coli DmsD -

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Basic information

Entry
Database: PDB / ID: 3cw0
TitleE.coli DmsD
ComponentsTwin-arginine leader-binding protein dmsD
KeywordsCHAPERONE / DmsD / Alpha-helices / Membrane
Function / homology
Function and homology information


signal sequence binding / : / protein maturation / plasma membrane / cytoplasm
Similarity search - Function
Tat proofreading chaperone DmsD / Tat proofreading chaperone DmsD-type / : / TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tat proofreading chaperone DmsD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsRamasamy, S. / Clemons, W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the twin-arginine signal-binding protein DmsD from Escherichia coli.
Authors: Ramasamy, S.K. / Clemons, W.M.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Twin-arginine leader-binding protein dmsD
B: Twin-arginine leader-binding protein dmsD
C: Twin-arginine leader-binding protein dmsD
D: Twin-arginine leader-binding protein dmsD


Theoretical massNumber of molelcules
Total (without water)94,8874
Polymers94,8874
Non-polymers00
Water9,170509
1
A: Twin-arginine leader-binding protein dmsD


Theoretical massNumber of molelcules
Total (without water)23,7221
Polymers23,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Twin-arginine leader-binding protein dmsD


Theoretical massNumber of molelcules
Total (without water)23,7221
Polymers23,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Twin-arginine leader-binding protein dmsD


Theoretical massNumber of molelcules
Total (without water)23,7221
Polymers23,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Twin-arginine leader-binding protein dmsD


Theoretical massNumber of molelcules
Total (without water)23,7221
Polymers23,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.449, 97.449, 210.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Twin-arginine leader-binding protein dmsD


Mass: 23721.865 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dmsD, ynfI / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P69853
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M Ammonium sulphate, 0.1M HEPES, 0.5% PEG8K, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.54 Å
DetectorDate: Jan 5, 2008
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→97.59 Å / Num. obs: 55317 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.383.90.389199.7
2.38-2.483.90.305199.8
2.48-2.593.90.259199.8
2.59-2.733.90.347199.9
2.73-2.93.90.155199.9
2.9-3.123.90.109199.9
3.12-3.433.90.118199.9
3.43-3.933.90.1081100
3.93-4.953.90.0391100
4.95-303.90.032199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
APEXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→88.4 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.157 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23968 2029 5 %RANDOM
Rwork0.19449 ---
obs0.19675 38472 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.112 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.4→88.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 0 509 7097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226812
X-RAY DIFFRACTIONr_bond_other_d0.0020.024572
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9329320
X-RAY DIFFRACTIONr_angle_other_deg0.945311060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.23923.735332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.955151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5391540
X-RAY DIFFRACTIONr_chiral_restr0.0810.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021480
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5761.54080
X-RAY DIFFRACTIONr_mcbond_other0.1241.51600
X-RAY DIFFRACTIONr_mcangle_it1.09826552
X-RAY DIFFRACTIONr_scbond_it1.88932732
X-RAY DIFFRACTIONr_scangle_it3.0194.52768
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 134 -
Rwork0.262 2810 -
obs--99.63 %
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)
12.1717-0.4308-0.42370.9533-0.28322.169-0.00930.0871-0.0679-0.06510.02170.05780.0543-0.1105-0.01240.027-0.01410.03280.0127-0.01670.064638.654-19.2113.069
21.5110.08180.28752.2558-0.15042.2592-0.0410.04430.0745-0.02020.10820.017-0.22930.0219-0.06710.0266-0.00420.01250.00640.00210.022229.72412.20118.209
31.7688-0.2747-0.25752.15650.69043.570.1660.0787-0.06970.07570.1489-0.36930.10750.4295-0.31480.02840.0222-0.02680.0653-0.05990.087660.70322.43911.969
42.36440.27770.06291.5320.15721.6920.0218-0.04780.0648-0.0242-0.031-0.14580.07590.08320.00930.00890.01040.02040.01590.01710.116469.735-9.1647.446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 204
2X-RAY DIFFRACTION2B2 - 204
3X-RAY DIFFRACTION3C2 - 204
4X-RAY DIFFRACTION4D2 - 204

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