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- PDB-4hkh: Structure of the Hcp1 protein from E. coli EAEC 042 pathovar, mut... -

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Basic information

Entry
Database: PDB / ID: 4hkh
TitleStructure of the Hcp1 protein from E. coli EAEC 042 pathovar, mutants N93W-S158W
ComponentsPutative type VI secretion protein
KeywordsPROTEIN BINDING / beta sandwich / tube of T6SS
Function / homology: / Hcp1-like / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp / Pnp Oxidase; Chain A / Roll / Mainly Beta / Type VI secretion protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsDouzi, B. / Spinelli, S. / Derrez, E. / Blangy, S. / Brunet, Y.R. / Cascales, E. / Cambillau, C.
CitationJournal: To be Published
Title: Structure of the Hcp1 protein from E. coli EAEC 042 pathovar, mutants N93W-S158W
Authors: Douzi, B. / Spinelli, S. / Derrez, E. / Blangy, S. / Brunet, Y.R. / Cascales, E. / Cambillau, C.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative type VI secretion protein
B: Putative type VI secretion protein
D: Putative type VI secretion protein
E: Putative type VI secretion protein
F: Putative type VI secretion protein
G: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,29317
Polymers118,2376
Non-polymers1,05711
Water13,007722
1
A: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9944
Polymers19,7061
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9944
Polymers19,7061
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8983
Polymers19,7061
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8983
Polymers19,7061
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Putative type VI secretion protein


Theoretical massNumber of molelcules
Total (without water)19,7061
Polymers19,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Putative type VI secretion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,7061
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.210, 145.890, 89.850
Angle α, β, γ (deg.)90.00, 103.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Putative type VI secretion protein


Mass: 19706.094 Da / Num. of mol.: 6 / Fragment: Hcp1 / Mutation: N93W, S158W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EAEC 042 / Gene: EC042_4529, Hcp1 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3GUW0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 14% PEG 3350, 50 mM bis-TRIS propane, 0.1 M Mg-formate , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 28, 2012 / Details: Si[111] monochromator crystal
RadiationMonochromator: Si[111] monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 116904 / Num. obs: 116904 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 20.46 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.095 / Net I/σ(I): 8.1
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2 / Num. unique all: 11432 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3HE1

3he1


Resolution: 1.69→43.7 Å / Cor.coef. Fo:Fc: 0.9286 / Cor.coef. Fo:Fc free: 0.9253 / SU R Cruickshank DPI: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 5862 5.02 %RANDOM
Rwork0.1802 ---
obs0.181 116811 99.42 %-
all-116811 --
Displacement parametersBiso mean: 27.66 Å2
Baniso -1Baniso -2Baniso -3
1-4.5389 Å20 Å20.4176 Å2
2--5.7973 Å20 Å2
3----10.3361 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.69→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 55 722 7679
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017253HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.149875HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d02479SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes01027HARMONIC5
X-RAY DIFFRACTIONt_it07253HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.1
X-RAY DIFFRACTIONt_other_torsion16.95
X-RAY DIFFRACTIONt_chiral_improper_torsion0949SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact08371SEMIHARMONIC4
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2533 403 4.69 %
Rwork0.2286 8189 -
all0.2298 8592 -
obs--99.42 %
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)
10.59680.2972-0.06451.32120.01270.3267-0.0069-0.01550.07020.0076-0.0026-0.01410.0169-0.00960.0095-0.03760.00010.00320.0093-0.0021-0.04235.8417-13.008120.4607
20.8905-0.5716-0.06560.93610.01670.5273-0.0179-0.00540.0720.0487-0.00720.00680.0255-0.00250.0251-0.0433-0.00590.0024-0.01390.0012-0.008533.121215.444720.4345
31.549-0.0894-0.04460.2429-0.07810.474-0.0094-0.03350.0446-0.0090.0108-0.02420.0139-0.0027-0.0014-0.03880.0064-0.0024-0.01610.0003-0.01027.374626.404320.7752
40.73420.23280.05171.45290.00470.42970.0078-0.0258-0.06670.0062-0.01360.0374-0.00560.03490.0058-0.03090.0012-0.00770.0170.0011-0.058-15.5779.372920.6156
50.7594-0.66180.08771.25820.02390.44080.0025-0.0053-0.06810.0244-0.011-0.0032-0.01850.01840.0085-0.051-0.0076-0.0027-0.0139-0.0052-0.0073-11.5846-18.085320.4756
61.4559-0.1260.02260.31750.16510.6312-0.0019-0.0352-0.0106-0.0001-0.0021-0.0158-0.0094-0.02510.004-0.03810.0061-0.0041-0.01020.0008-0.025213.8854-29.131920.1897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|158 }A2 - 158
2X-RAY DIFFRACTION2{ B|3 - B|158 }B3 - 158
3X-RAY DIFFRACTION3{ D|3 - D|158 }D3 - 158
4X-RAY DIFFRACTION4{ E|2 - E|159 }E2 - 159
5X-RAY DIFFRACTION5{ F|2 - F|157 }F2 - 157
6X-RAY DIFFRACTION6{ G|3 - G|158 }G3 - 158

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