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- PDB-4rsw: The structure of the effector protein from Pseudomonas syringae p... -

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Basic information

Entry
Database: PDB / ID: 4rsw
TitleThe structure of the effector protein from Pseudomonas syringae pv. syringae strain 61
ComponentsHopA1
KeywordsSIGNALING PROTEIN / alpha/beta fold / effector
Function / homologyHopA1 effector protein / HopA1 effector protein family / HopA1
Function and homology information
Biological speciesPseudomonas syringae pv. syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPark, Y. / Shin, I. / Rhee, S.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of the effector protein HopA1 from Pseudomonas syringae
Authors: Park, Y. / Shin, I. / Rhee, S.
History
DepositionNov 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HopA1
B: HopA1


Theoretical massNumber of molelcules
Total (without water)57,6022
Polymers57,6022
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-7 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.522, 62.522, 156.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein HopA1 / Effector protein


Mass: 28801.201 Da / Num. of mol.: 2 / Fragment: UNP residues 120-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. syringae (bacteria)
Strain: 61 / Gene: hopA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83YM3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.66 Å3/Da / Density % sol: 53.79 % / Mosaicity: 0.809 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 56.43 %(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97946, 0.97960, 0.97178
DetectorType: ADSC QUANTUM 270 / Detector: CCD
RadiationMonochromator: DCM Si (111) Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.97961
30.971781
ReflectionResolution: 1.9→50 Å / Num. obs: 47054 / % possible obs: 99.6 % / Redundancy: 14.8 % / Biso Wilson estimate: 28.42 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.065 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.97150.96247020.855100
1.97-2.0515.10.66146880.885100
2.05-2.1415.10.46247220.908100
2.14-2.2515.10.31647290.931100
2.25-2.3915.20.24247030.969100
2.39-2.5815.20.18747061.031100
2.58-2.8415.20.13847411.084100
2.84-3.2515.10.10347111.2100
3.25-4.0914.20.08147141.27699.6
4.09-5012.40.0846381.6496.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→33.74 Å / FOM work R set: 0.8505 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2264 1991 4.24 %
Rwork0.1951 --
obs0.1964 47009 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.13 Å2 / Biso mean: 30.26 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 0 358 4336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084048
X-RAY DIFFRACTIONf_angle_d1.0965456
X-RAY DIFFRACTIONf_chiral_restr0.071590
X-RAY DIFFRACTIONf_plane_restr0.004726
X-RAY DIFFRACTIONf_dihedral_angle_d14.891574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8996-1.94710.27261420.25853194333699
1.9471-1.99970.26731410.255632413382100
1.9997-2.05860.27461440.223631963340100
2.0586-2.1250.27411350.218932133348100
2.125-2.20090.24831400.212632453385100
2.2009-2.2890.2581430.213432043347100
2.289-2.39320.25771440.210232363380100
2.3932-2.51930.2671490.215332163365100
2.5193-2.67710.22771430.204232163359100
2.6771-2.88370.22471420.200932153357100
2.8837-3.17370.221400.190332653405100
3.1737-3.63250.1811410.173732093350100
3.6325-4.57470.19791430.16323207335099
4.5747-33.74510.23021440.19753161330597
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)
10.77660.51820.46851.64080.67190.455-0.1120.0948-0.1149-0.28940.0791-0.128-0.08930.1193-0.02920.2235-0.00960.06040.15420.00470.12394.8827-20.9769-4.2758
21.2644-0.1756-0.19770.4433-0.00960.1481-0.09450.06710.2505-0.40560.0167-0.1827-0.10.07290.0290.3176-0.03490.02370.15130.03130.20256.9897-9.1589-5.173
30.90320.3063-0.24350.72530.15241.1316-0.0884-0.19950.1610.0119-0.0680.1764-0.07780.0137-0.29420.19050.0032-0.00530.1508-0.05710.1877-5.4301-12.35918.1202
40.31730.0386-0.09490.297-0.00990.2340.08410.0354-0.0147-0.0858-0.0221-0.2071-0.1413-0.04210.0110.17440.0213-0.04760.17110.02070.22298.1005-36.34641.7085
50.42160.1806-0.12320.48250.04360.5890.11090.09510.0206-0.2582-0.23550.4336-0.1665-0.12880.0140.23570.0511-0.08120.1888-0.06010.2403-17.7527-33.6327-8.2669
60.4556-0.10620.07890.30070.07510.35720.09750.0387-0.1628-0.0823-0.11360.1649-0.0187-0.0471-0.00670.175-0.0099-0.04520.1041-0.02970.176-8.5915-46.5633-4.56
70.51050.2509-0.44350.3432-0.17930.40150.0661-0.1382-0.1090.1096-0.1144-0.0731-0.0719-0.0731-00.2256-0.01-0.04310.17610.03450.21014.6017-43.27138.1711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 120 through 219 )A0
2X-RAY DIFFRACTION2chain A and (resid 220 through 298 )A0
3X-RAY DIFFRACTION3chain A and (resid 299 through 374 )A0
4X-RAY DIFFRACTION4chain B and (resid 120 through 163 )B0
5X-RAY DIFFRACTION5chain B and (resid 164 through 219 )B0
6X-RAY DIFFRACTION6chain B and (resid 220 through 298 )B0
7X-RAY DIFFRACTION7chain B and (resid 299 through 374 )B0

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