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- PDB-6e8a: Crystal structure of DcrB from Salmonella enterica at 1.92 Angstr... -

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Basic information

Entry
Database: PDB / ID: 6e8a
TitleCrystal structure of DcrB from Salmonella enterica at 1.92 Angstroms resolution
ComponentsDUF1795 domain-containing protein
KeywordsUNKNOWN FUNCTION / Mog1/PsbP-like fold lipoprotein
Function / homologyInner membrane lipoprotein DcrB/EagT6 / DcrB / Mog1/PsbP, alpha/beta/alpha sandwich / DUF1795 domain-containing protein / Putative inner membrane lipoprotein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsRasmussen, D.M. / Soens, R.W. / Bhattacharyya, B. / May, J.F.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: The structure of DcrB, a lipoprotein from Salmonella enterica, reveals flexibility in the N-terminal segment of the Mog1p/PsbP-like fold.
Authors: Rasmussen, D.M. / Soens, R.W. / Davie, T.J. / Vaneerd, C.K. / Bhattacharyya, B. / May, J.F.
History
DepositionJul 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF1795 domain-containing protein
B: DUF1795 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,9322
Polymers33,9322
Non-polymers00
Water48627
1
A: DUF1795 domain-containing protein

A: DUF1795 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,9322
Polymers33,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area5110 Å2
ΔGint-43 kcal/mol
Surface area13510 Å2
MethodPISA
2
B: DUF1795 domain-containing protein

B: DUF1795 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,9322
Polymers33,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4720 Å2
ΔGint-39 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.715, 41.715, 533.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 40 - 183 / Label seq-ID: 11 - 154

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein DUF1795 domain-containing protein


Mass: 16966.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: C4822_00510, C4872_00325, DD95_06545 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0J5EW41, UniProt: Q7CPJ3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 2.0 M ammonium sulfate, 100 mM Tris pH 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97851 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.92→44.5 Å / Num. obs: 22978 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 36.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.017 / Rrim(I) all: 0.099 / Net I/σ(I): 21.2
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 32.7 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1086 / CC1/2: 0.885 / Rpim(I) all: 0.31 / Rrim(I) all: 1.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.92→44.49 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.959 / SU B: 9.312 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1188 5.2 %RANDOM
Rwork0.2219 ---
obs0.2226 21790 99.2 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 235.48 Å2 / Biso mean: 68.173 Å2 / Biso min: 31.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----1.42 Å2
Refinement stepCycle: final / Resolution: 1.92→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 27 2226
Biso mean---50.39 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0142218
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172083
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.6493010
X-RAY DIFFRACTIONr_angle_other_deg0.8671.6384898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70826.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05115412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.293156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
Refine LS restraints NCS

Ens-ID: 1 / Number: 3765 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.915→1.965 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 87 -
Rwork0.268 1534 -
all-1621 -
obs--100 %
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)
10.61461.3671-1.14726.0592-0.42983.7125-0.0774-0.0442-0.153-0.20570.0129-0.51090.05960.26680.06450.3829-0.124-0.00870.2624-0.00710.315221.868-26.21241.825
25.1052-1.3745-2.65724.9011.97446.3881-0.00250.2624-0.60340.1425-0.1128-0.25160.3951-0.02710.11530.2237-0.09470.00080.1081-0.02730.190929.919-12.9539.841
37.64940.29631.50512.2894-0.3364.0919-0.20320.4633-0.3623-0.30930.2224-0.2137-0.1149-0.0079-0.01920.2982-0.11910.06820.1461-0.00930.063323.277-8.228.17
424.695-7.8577-10.18887.32674.4556.956-0.00640.0468-0.0492-0.2140.2534-0.6210.01320.2012-0.2470.1875-0.10030.04660.1163-0.04920.091631.463-9.58134.101
526.8635-0.6761.70224.23320.53453.50180.12810.20760.2298-0.3296-0.05530.3305-0.39750.1382-0.07280.2646-0.1051-0.0170.0693-0.02350.155926.4041.54336.992
65.08736.8719-9.25112.0183-7.049332.1898-1.06630.0683-0.1959-1.2890.47640.44573.294-1.0720.58992.1681-0.5163-0.38541.19010.22550.75375.229-11.224-2.85
72.7462.2287-6.11114.9815-6.457722.7436-0.34820.6029-0.2263-0.29750.10150.4011-0.0334-1.47880.24670.4163-0.02270.0440.4850.01920.19586.240.188.666
824.4491-6.8099-1.763616.9782-0.14618.6856-0.2830.8599-1.161-0.23770.07290.49741.1180.63390.21010.5063-0.00630.05250.4422-0.02520.061215.788-11.7814.101
99.1897-1.80060.34684.5727-2.665111.2459-0.07670.42050.3290.3114-0.0675-0.0297-0.76720.14630.14410.3876-0.08110.01110.26480.04570.020511.9760.12815.033
1018.5542-8.0685-3.65019.5952-2.355512.4142-0.1221-0.58570.62190.8648-0.2329-1.2913-2.06581.43840.35511.1462-0.3395-0.23670.3977-0.07350.434417.4718.26113.804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 67
2X-RAY DIFFRACTION2A68 - 94
3X-RAY DIFFRACTION3A95 - 149
4X-RAY DIFFRACTION4A150 - 165
5X-RAY DIFFRACTION5A166 - 185
6X-RAY DIFFRACTION6B40 - 69
7X-RAY DIFFRACTION7B70 - 99
8X-RAY DIFFRACTION8B100 - 115
9X-RAY DIFFRACTION9B116 - 165
10X-RAY DIFFRACTION10B166 - 184

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