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- PDB-4dn6: Crystal structure of a putative pilus assembly protein (cpaE) fro... -

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Basic information

Entry
Database: PDB / ID: 4dn6
TitleCrystal structure of a putative pilus assembly protein (cpaE) from Burkholderia thailandensis E264 at 2.80 A resolution
ComponentsPutative pilus assembly protein CpaE
KeywordsSIGNALING PROTEIN / Response regulator receiver domain / CHEY-related protein / signal transduction / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
AAA domain / AAA domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative pilus assembly protein CpaE
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG) / Shapiro, L.
CitationJournal: To be published
Title: Crystal structure of a putative pilus assembly protein (cpaE) from Burkholderia thailandensis E264 at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG) / Shapiro, L.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative pilus assembly protein CpaE
B: Putative pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)32,6362
Polymers32,6362
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.114, 116.114, 45.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsCRYSTAL PACKING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative pilus assembly protein CpaE


Mass: 16317.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: cpaE, BTH_II2273 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q2T2Y8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 1-127 OF THE FULL LENGTH PROTEIN.

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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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10.0% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011
Details: FLAT MIRROR (VERTICAL FOCUSING); SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.918371
ReflectionResolution: 2.8→29.57 Å / Num. obs: 8094 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.89 % / Biso Wilson estimate: 93.904 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.8-2.90.7951.5857591484198.5
2.9-3.020.4742.758411495199.4
3.02-3.150.32452061390199.6
3.15-3.320.2256.153291491199.3
3.32-3.520.10910.658271437199.6
3.52-3.790.09814.352731395194.3
3.79-4.170.05620.458431489199.5
4.17-4.770.04227.651241429198.3
4.77-5.980.03830.557961479199.8
5.98-29.570.02538.557401506198

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.57 Å / Cor.coef. Fo:Fc: 0.9418 / Cor.coef. Fo:Fc free: 0.9314 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. MAD EXPERIMENTAL PHASES IN THE FORM OF HENDRICKSON-LATTMAN COEFFICIENTS WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 374 4.64 %RANDOM
Rwork0.2131 ---
obs0.2143 8066 98.96 %-
Displacement parametersBiso max: 185.33 Å2 / Biso mean: 84.859 Å2 / Biso min: 49.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.0003 Å20 Å20 Å2
2--0.0003 Å20 Å2
3----0.0005 Å2
Refine analyzeLuzzati coordinate error obs: 0.527 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 0 16 1854
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d905SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes283HARMONIC5
X-RAY DIFFRACTIONt_it1866HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion259SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2012SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1866HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2532HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion2.31
LS refinement shellResolution: 2.8→3.13 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2917 109 4.86 %
Rwork0.2516 2134 -
all0.2538 2243 -
obs--98.96 %
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)
18.61331.1144-3.253.1553-1.04814.89630.1108-0.3699-0.0179-0.0551-0.3997-0.46620.03860.38550.2889-0.1916-0.0556-0.0189-0.1335-0.0815-0.032192.75577.67249.2657
27.74764.69134.30366.02125.62516.36790.03630.1970.4522-0.35560.03230.1425-0.37110.2588-0.0686-0.12140.0252-0.1128-0.2859-0.0481-0.027977.3511-10.0362-1.814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-3 - 122}A-3 - 122
2X-RAY DIFFRACTION2{B|1 - 122}B1 - 122

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