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- PDB-4n0p: Crystal structure of a pilus assembly protein CpaE (CC_2943) from... -

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Basic information

Entry
Database: PDB / ID: 4n0p
TitleCrystal structure of a pilus assembly protein CpaE (CC_2943) from Caulobacter crescentus CB15 at 1.75 A resolution (PSI Community Target, Shapiro)
ComponentsPilus assembly protein CpaE
KeywordsSIGNALING PROTEIN / Response regulator receiver domain / PF00072 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyAAA domain / AAA domain / CheY-like superfamily / Response regulator / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Pilus assembly protein CpaE
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a pilus assembly protein CpaE (CC_2943) from Caulobacter crescentus CB15 at 1.75 A resolution (PSI Community Target, Shapiro)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pilus assembly protein CpaE
B: Pilus assembly protein CpaE
C: Pilus assembly protein CpaE
D: Pilus assembly protein CpaE
E: Pilus assembly protein CpaE
F: Pilus assembly protein CpaE
G: Pilus assembly protein CpaE
H: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)133,1448
Polymers133,1448
Non-polymers00
Water10,863603
1
A: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Pilus assembly protein CpaE


Theoretical massNumber of molelcules
Total (without water)16,6431
Polymers16,6431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.600, 112.780, 73.880
Angle α, β, γ (deg.)90.000, 94.120, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Pilus assembly protein CpaE


Mass: 16643.037 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: CC_2943 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q9A495
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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 124-255 OF THE FULL LENGTH PROTEIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.0539.92
2
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 1000; 0.2M Ammonium Acetate, 0.1M TRIS pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 295K
Experiment crystal cryo treatment
Crystal-IDCooling detailsFinal solution detailsSoaking details
1Direct immersion in liquid nitrogen30% (w/v) PEG-4000 in precipitant
2Direct immersion in liquid nitrogen30% (w/v) PEG-4000, 0.007 M thimerosal in precipitantFirst PEG-4000 was added to 30% (w/v) in precipitant. Thimerosal was then added to a final concentration of 0.007 M and after 70 minutes the crystal was harvested.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-210.9795
SYNCHROTRONSSRL BL12-221.008
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELJan 26, 2012Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
DECTRIS PILATUS 6M2PIXELJan 26, 2012Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.0081
ReflectionResolution: 1.75→47.271 Å / Num. obs: 105477 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 26.669 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.83.80.7971.729351779697.7
1.8-1.843.70.6532.227707748896.7
1.84-1.93.50.4683.124902717795.2
1.9-1.963.90.3444.628058726199.3
1.96-2.023.90.2616.227649700599
2.02-2.093.90.2187.426759679298.9
2.09-2.173.90.1679.125921656498.6
2.17-2.263.90.1321124462625498.3
2.26-2.363.80.10612.722171589596.3
2.36-2.473.70.09214.221114566296.9
2.47-2.6140.07517.322338554799.4
2.61-2.7740.06519.120764524499.3
2.77-2.963.90.05521.919021488798.7
2.96-3.23.80.04524.917064454698.4
3.2-3.53.40.0426.613572401194.6
3.5-3.913.70.03630.514248380398.5
3.91-4.523.80.03532.412576333498.2
4.52-5.533.70.03432.510353283398.3
5.53-7.833.50.03431.37395214095.3
7.83-47.2713.90.03335.54878123897.9

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.75→47.271 Å / Cor.coef. Fo:Fc: 0.9574 / Cor.coef. Fo:Fc free: 0.9479 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 5254 4.98 %RANDOM
Rwork0.1807 ---
obs0.182 105434 97.83 %-
Displacement parametersBiso max: 133.74 Å2 / Biso mean: 33.927 Å2 / Biso min: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.1644 Å20 Å22.5095 Å2
2---4.2398 Å20 Å2
3---4.0754 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.75→47.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7983 0 0 603 8586
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3995SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes201HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1285HARMONIC5
X-RAY DIFFRACTIONt_it8369HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1142SEMIHARMONIC5
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_contact10083SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8369HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11452HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion2.79
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2863 383 4.93 %
Rwork0.2411 7393 -
all0.2433 7776 -
obs--97.83 %

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