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- PDB-4djm: Crystal structure of the E. coli chaperone DraB -

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Basic information

Entry
Database: PDB / ID: 4djm
TitleCrystal structure of the E. coli chaperone DraB
ComponentsDraB
KeywordsCHAPERONE / DraB / Pili
Function / homology
Function and homology information


pilus organization / chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Periplasmic chaperone / DraB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDauter, Z. / Piatek, R. / Dauter, M. / Brzuszkiewicz, A.
CitationJournal: To be Published
Title: Crystal structure of the uropathogenic Escherichia coli chaperone DraB
Authors: Dauter, Z. / Piatek, R. / Dauter, M. / Brzuszkiewicz, A.
History
DepositionFeb 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DraB
B: DraB
C: DraB
D: DraB
E: DraB
F: DraB
G: DraB
H: DraB


Theoretical massNumber of molelcules
Total (without water)209,2338
Polymers209,2338
Non-polymers00
Water00
1
A: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DraB


Theoretical massNumber of molelcules
Total (without water)26,1541
Polymers26,1541
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.450, 98.410, 100.880
Angle α, β, γ (deg.)84.20, 89.80, 83.80
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DraB


Mass: 26154.090 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: draB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q7BG37, UniProt: Q6S361*PLUS

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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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein solution: 15 mg/ml protein, 20 mM Tris pH 8.0, 200 mM NaCl, 10 % glycerol well solution: 200 mM MgCl2, 100 mM Bis-Tris pH 6.5, 25% PEG3350 protein and well solutions mixed 1:1, VAPOR ...Details: protein solution: 15 mg/ml protein, 20 mM Tris pH 8.0, 200 mM NaCl, 10 % glycerol well solution: 200 mM MgCl2, 100 mM Bis-Tris pH 6.5, 25% PEG3350 protein and well solutions mixed 1:1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9724 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2009 / Details: mirrors
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 76049 / Num. obs: 74832 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CO6

2co6


Resolution: 2.52→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.881 / SU B: 20.307 / SU ML: 0.208 / Isotropic thermal model: Isotropic, + TLS / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26871 1489 2 %RANDOM
Rwork0.20581 ---
all0.20709 73265 --
obs0.20709 73265 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.597 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å2-0.12 Å20.87 Å2
2--1.21 Å2-0.67 Å2
3----3.06 Å2
Refinement stepCycle: LAST / Resolution: 2.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12557 0 0 0 12557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02212853
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9817470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.97451585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57623.638547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.804152144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.96315102
X-RAY DIFFRACTIONr_chiral_restr0.1480.21949
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0229750
X-RAY DIFFRACTIONr_mcbond_it2.73238044
X-RAY DIFFRACTIONr_mcangle_it4.673513112
X-RAY DIFFRACTIONr_scbond_it6.85564809
X-RAY DIFFRACTIONr_scangle_it9.26484358
LS refinement shellResolution: 2.516→2.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 90 -
Rwork0.265 4746 -
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)
11.21481.16511.19793.60561.68581.83080.0912-0.1082-0.01790.2674-0.26810.35150.29960.07570.17690.2957-0.05570.08430.1640.0290.12348.117379.158789.7367
23.3044-0.2317-1.25262.76460.40044.76170.34910.1018-0.0523-0.0379-0.1820.0873-0.3415-0.024-0.16710.1881-0.00350.04110.03390.03740.158157.30997.070872.1698
30.91361.0823-0.8474.0458-1.40481.02370.0763-0.0489-0.02810.4163-0.06970.0624-0.3060.1042-0.00660.2619-0.0278-0.01640.1125-0.00070.196136.651637.173885.7132
41.941-0.4466-1.14122.7889-0.97813.0069-0.18610.5424-0.0831-0.66750.06810.22670.2953-0.37730.1180.267-0.0792-0.14770.2766-0.010.205629.833419.346165.588
51.676-1.22780.93961.7439-0.62211.0395-0.0547-0.089-0.0972-0.00020.0190.0130.0071-0.02760.03570.13920.01020.04240.18490.00710.188832.766174.104957.7055
62.3320.8324-2.00543.90610.78715.3929-0.0002-0.79350.45340.1640.2636-0.3873-0.1640.2151-0.26340.06520.1126-0.04520.5641-0.27070.274124.231793.218173.9869
70.7956-0.7256-0.54372.48660.22740.44590.04630.0470.0752-0.31630.05780.1119-0.0746-0.0344-0.10410.2775-0.008-0.04150.19040.02050.166549.281733.781966.2342
82.57770.40650.8163.39431.52174.3482-0.0077-0.29010.02090.37460.0062-0.06810.20680.04910.00150.08630.0329-0.06050.2023-0.00170.129359.374521.999589.3344
91.3955-1.0915-1.05441.86480.42911.02970.0092-0.01380.1199-0.0953-0.0888-0.2294-0.0607-0.04610.07960.2320.0479-0.08990.2384-0.10870.229621.275722.781310.1112
101.8677-0.20540.82743.6944-0.42368.74050.1029-0.59140.09110.0879-0.02140.1840.1741-0.3953-0.08150.0111-0.03060.01610.36550.05280.124731.53917.352229.1741
111.6955-1.52810.66022.7249-0.0691.17840.04150.2046-0.0333-0.37110.0645-0.13550.11610.0973-0.1060.1878-0.02490.04740.1884-0.01080.13884.343763.773913.8164
121.49030.1892-0.33671.5108-0.47563.0256-0.0199-0.12450.04750.08980.023-0.0278-0.2466-0.1219-0.0030.08460.04540.00840.16350.01450.2007-3.924679.358835.2866
130.750.2404-0.72462.2891-1.01681.26010.0281-0.11140.03710.2053-0.1431-0.1732-0.12730.0440.1150.2373-0.0346-0.06850.11860.01170.17916.036126.868542.1995
142.2035-0.47331.39882.7632-0.10414.42050.1060.16550.0695-0.0936-0.1406-0.07270.01780.02210.03460.1688-0.01380.01070.06560.04650.1632-1.25545.270327.7359
150.37710.48210.30242.12540.37010.5835-0.0665-0.0472-0.11080.04890.1616-0.08830.08270.0627-0.09510.16340.04250.01560.19310.00770.214717.003267.957633.3649
163.4203-0.6111-0.29924.0440.0872.8884-0.22440.4857-0.0694-0.65310.3153-0.306-0.04110.2312-0.09090.2038-0.1610.13150.2389-0.07310.121425.497981.767511.5734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 152
2X-RAY DIFFRACTION2A153 - 237
3X-RAY DIFFRACTION3B16 - 152
4X-RAY DIFFRACTION4B153 - 237
5X-RAY DIFFRACTION5C17 - 152
6X-RAY DIFFRACTION6C153 - 237
7X-RAY DIFFRACTION7D16 - 152
8X-RAY DIFFRACTION8D153 - 238
9X-RAY DIFFRACTION9E19 - 152
10X-RAY DIFFRACTION10E153 - 237
11X-RAY DIFFRACTION11F16 - 152
12X-RAY DIFFRACTION12F153 - 237
13X-RAY DIFFRACTION13G17 - 152
14X-RAY DIFFRACTION14G153 - 237
15X-RAY DIFFRACTION15H16 - 152
16X-RAY DIFFRACTION16H153 - 237

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