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- PDB-2p7n: Crystal structure of the Pathogenicity island 1 effector protein ... -

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Basic information

Entry
Database: PDB / ID: 2p7n
TitleCrystal structure of the Pathogenicity island 1 effector protein from Chromobacterium violaceum. Northeast Structural Genomics Consortium (NESGC) target CvR69.
ComponentsPathogenicity island 1 effector protein
KeywordsCELL INVASION / cvr69 / Pathogenicity island 1 effector protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyIpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Translocator protein BipD
Function and homology information
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBenach, J. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Benach, J. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Pathogenicity island 1 effector protein from Chromobacterium violaceum. Northeast Structural Genomics Consortium (NESGC) target CvR69.
Authors: Benach, J. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / ...Authors: Benach, J. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Cunningham, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Pathogenicity island 1 effector protein


Theoretical massNumber of molelcules
Total (without water)43,7571
Polymers43,7571
Non-polymers00
Water27015
1
A: Pathogenicity island 1 effector protein

A: Pathogenicity island 1 effector protein


Theoretical massNumber of molelcules
Total (without water)87,5142
Polymers87,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)55.026, 66.981, 194.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsA dimer can be constructed by applying the symmetry operation (-X,-Y,Z)

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Components

#1: Protein Pathogenicity island 1 effector protein


Mass: 43757.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Strain: DSM 30191, IFO 12614, JCM 1249, NCIB 9131 / Gene: sipD, CV_2617 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7NUT0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 150 mM Sodium acetate pH 4.6, 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912, 0.97897, 0.96862
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 2, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979121
20.978971
30.968621
Reflection

D res high: 2.6 Å / D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
7.5112.31614770.0891.442149599.9
7.5211.41620710.0941.352159899.9
7.4313.91578460.0871.692123799.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.310.0381.0857.3
4.455.610010.0481.0447.7
3.884.4510010.0651.037.7
3.533.8810010.1341.7726.9
3.283.5310010.1281.1547.7
3.083.2810010.1871.3087.7
2.933.0810010.271.4917.7
2.82.9310010.3681.5417.7
2.692.810010.5262.2557.5
2.62.6910010.6652.0527.1
5.65099.520.0380.9637.4
4.455.610020.0491.0087.8
3.884.4510020.0671.1497.7
3.533.8810020.1361.437.1
3.283.5310020.1361.0727.7
3.083.2810020.211.287.7
2.933.0810020.3021.4557.7
2.82.9310020.4311.4897.7
2.692.810020.5821.5677.4
2.62.6910020.7641.5236.8
5.65098.330.0381.1357.2
4.455.610030.0471.0997.7
3.884.4510030.0661.2247.6
3.533.8899.630.1281.8986.1
3.283.5310030.1281.4947.7
3.083.2810030.1841.4047.7
2.933.0810030.271.9117.7
2.82.9310030.3591.9817.7
2.692.810030.5162.557.6
2.62.6910030.6722.4677.3
ReflectionResolution: 2.6→50 Å / Num. obs: 21495 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.089 / Χ2: 1.443 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.697.10.66521592.052100
2.69-2.87.50.52621542.255100
2.8-2.937.70.36821341.541100
2.93-3.087.70.2721551.491100
3.08-3.287.70.18721241.308100
3.28-3.537.70.12821671.154100
3.53-3.886.90.13421481.772100
3.88-4.457.70.06521561.03100
4.45-5.67.70.04821621.044100
5.6-507.30.03821361.08599.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / FOM work R set: 0.779 / σ(F): 485 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflection
Rfree0.298 1496 8.8 %
Rwork0.248 --
obs-15650 91.7 %
Solvent computationBsol: 11.085 Å2
Displacement parametersBiso mean: 51.277 Å2
Baniso -1Baniso -2Baniso -3
1--6.022 Å20 Å20 Å2
2---19.066 Å20 Å2
3---25.088 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2514 0 0 15 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.5421.5
X-RAY DIFFRACTIONc_scbond_it2.4512
X-RAY DIFFRACTIONc_mcangle_it2.6022
X-RAY DIFFRACTIONc_scangle_it3.932.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.830.5310.379385416
2.83-2.870.382630.411439502
2.87-2.90.436370.372430467
2.9-2.940.474430.389426469
2.94-2.980.403540.321442496
2.98-3.020.283370.322471508
3.02-3.070.316520.324487539
3.07-3.120.532540.35450504
3.12-3.170.427430.304480523
3.17-3.220.338430.259500543
3.22-3.280.337620.302450512
3.28-3.340.253430.254527570
3.34-3.410.312550.3470525
3.41-3.490.325480.26527575
3.49-3.570.272480.243498546
3.57-3.650.307480.227449497
3.65-3.750.304490.245455504
3.75-3.860.315560.218484540
3.86-3.990.24500.214523573
3.99-4.130.269570.209529586
4.13-4.290.295550.188505560
4.29-4.480.252450.228555600
4.48-4.720.31730.201491564
4.72-5.010.239680.225529597
5.01-5.390.278480.245534582
5.39-5.920.259680.273526594
5.92-6.750.37530.241542595
6.75-8.390.293600.241518578
8.39-200.213530.206532585
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.par
X-RAY DIFFRACTION2water_rep.param

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