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- PDB-4pwz: Crystal structure of TolB protein from Yersinia pestis CO92 -

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Basic information

Entry
Database: PDB / ID: 4pwz
TitleCrystal structure of TolB protein from Yersinia pestis CO92
ComponentsProtein TolB
KeywordsPROTEIN TRANSPORT / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold and beta propeller fold / translocation / Pal
Function / homology
Function and homology information


protein import / periplasmic space / cell cycle / cell division
Similarity search - Function
TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase ...TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Tol-Pal system protein TolB
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.732 Å
AuthorsMaltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of TolB protein from Yersinia pestis CO92
Authors: Maltseva, N. / Kim, Y. / Osipiuk, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Protein TolB
B: Protein TolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1927
Polymers88,5972
Non-polymers5965
Water9,962553
1
A: Protein TolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4052
Polymers44,2981
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein TolB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7885
Polymers44,2981
Non-polymers4904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.440, 95.813, 80.514
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protein TolB


Mass: 44298.422 Da / Num. of mol.: 2 / Fragment: UNP residues 23-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: tolB, y3055, YPO1124, YP_1032 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8ZGZ1

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Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 45.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 10% PEG5000 MME, 12% 1-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 81921 / Num. obs: 81921 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 17.29 Å2 / Rsym value: 0.06 / Net I/σ(I): 13.2
Reflection shellResolution: 1.73→1.75 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3562 / Rsym value: 0.607 / % possible all: 86.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
ARP/wARPmodel building
PHENIX(phenix.refine: dev_1593)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C5K

1c5k


Resolution: 1.732→30.74 Å / SU ML: 0.17 / Isotropic thermal model: MIXED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3993 5.01 %RANDOM
Rwork0.167 ---
all0.169 79632 --
obs0.169 79632 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9 Å2
Refinement stepCycle: LAST / Resolution: 1.732→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 37 553 6722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016762
X-RAY DIFFRACTIONf_angle_d1.2879276
X-RAY DIFFRACTIONf_dihedral_angle_d14.0032501
X-RAY DIFFRACTIONf_chiral_restr0.0691015
X-RAY DIFFRACTIONf_plane_restr0.0081246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.732-1.75230.25061070.21261816192368
1.7523-1.77370.24551140.20642161227581
1.7737-1.79610.28131050.20512285239085
1.7961-1.81980.23841180.19172453257190
1.8198-1.84470.2571390.19142515265494
1.8447-1.8710.26981500.18282568271895
1.871-1.8990.22941430.17712581272498
1.899-1.92860.19421630.18272663282699
1.9286-1.96020.25351360.17542660279699
1.9602-1.9940.21011160.178426852801100
1.994-2.03030.23681320.171427242856100
2.0303-2.06930.23221470.177326782825100
2.0693-2.11160.18581190.166326922811100
2.1116-2.15750.17731390.168726802819100
2.1575-2.20760.19811370.171926922829100
2.2076-2.26280.24571330.179527082857100
2.2628-2.3240.20331490.170726922841100
2.324-2.39230.21351400.169326892829100
2.3923-2.46950.22431520.178526792831100
2.4695-2.55780.20561490.177726762825100
2.5578-2.66010.19051470.180126992846100
2.6601-2.78110.2251360.175327282864100
2.7811-2.92760.17921480.181326592807100
2.9276-3.11090.22011530.182326902743100
3.1109-3.35080.19171590.174526822841100
3.3508-3.68750.17991460.154127202866100
3.6875-4.21990.1651370.146226932830100
4.2199-5.31220.1521370.125627512888100
5.3122-30.74480.17351420.15772720286299
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)
11.9861-0.38922.67031.7562-1.4338.09660.06650.1398-0.1933-0.07340.0594-0.11810.11010.1988-0.08190.03880.02130.05110.1395-00.187241.557111.534552.0796
21.84530.6585-0.21742.93310.18931.4163-0.0136-0.0449-0.07890.0418-0.0125-0.07560.01220.03980.03940.08160.02450.00090.08560.0090.094737.638317.876857.5883
31.71290.29270.34861.3608-0.13821.22210.0190.1137-0.2488-0.12720.0243-0.06290.1648-0.042-0.03540.146-0.00290.00250.0972-0.0160.092918.9177-7.556647.1393
41.93910.52610.22222.674-0.25532.6508-0.0802-0.0689-0.0111-0.14120.06490.16010.0065-0.22090.00710.13140.0013-0.02370.1334-0.00090.08754.02231.610135.6716
52.8451-0.3471-0.0182.2247-0.41152.9751-0.06940.2269-0.0534-0.2896-0.0267-0.12610.05490.2750.09060.1624-0.03990.01650.1394-0.01010.101924.59575.380235.2613
60.8949-0.899-0.07242.10550.10090.54730.04160.0280.1276-0.0949-0.0834-0.1676-0.02190.07650.02440.0827-0.0088-0.00740.11870.01950.130334.8866-16.964368.797
70.9891-0.148-0.48271.0636-0.37081.231-0.023-0.05460.02630.1030.02070.007-0.0828-0.06240.00420.09180.0022-0.0080.1022-0.02140.07979.8577-6.220580.4047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 344 )
5X-RAY DIFFRACTION5chain 'A' and (resid 345 through 430 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 198 )
7X-RAY DIFFRACTION7chain 'B' and (resid 199 through 430 )

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