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- PDB-3hsa: Crystal structure of pleckstrin homology domain (YP_926556.1) fro... -

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Basic information

Entry
Database: PDB / ID: 3hsa
TitleCrystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution
Componentspleckstrin homology domain
Keywordsstructural genomics / unknown function / YP_926556.1 / pleckstrin homology domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Protein of unknown function (DUF1696)
Function / homologyBacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain superfamily / Bacterial PH domain / PH-domain like / Roll / Mainly Beta / DI(HYDROXYETHYL)ETHER / bPH_1 domain-containing protein
Function and homology information
Biological speciesShewanella amazonensis SB2B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain.
Authors: Xu, Q. / Bateman, A. / Finn, R.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / ...Authors: Xu, Q. / Bateman, A. / Finn, R.D. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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: pleckstrin homology domain
B: pleckstrin homology domain
C: pleckstrin homology domain
D: pleckstrin homology domain
E: pleckstrin homology domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,82613
Polymers72,0615
Non-polymers7658
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-54 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.230, 129.490, 138.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
pleckstrin homology domain


Mass: 14412.244 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis SB2B (bacteria) / Gene: Sama_0678, YP_926556.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S3D0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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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

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.61 %
Description: THE STRUCTURE WAS SOLVED BY MAD METHOD USING FOUR DATASETS COLLECTED FROM TWO CRYSTALS. THE SHARP OUTPUT PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5.0000% polyethylene glycol 3000, 22.0000% polyethylene glycol 400, 10.0000% Glycerol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9792
SYNCHROTRONSSRL BL9-220.97920,0.97934,0.91837
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDMay 14, 2009Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDMay 14, 2009Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979341
30.918371
ReflectionResolution: 1.99→47.351 Å / Num. obs: 41702 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 22.653 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.18
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.99-2.060.5312.31488340751,299.1
2.06-2.140.40831459439491,298.4
2.14-2.240.3143.81555242331,298.1
2.24-2.360.2484.81540142091,299.5
2.36-2.510.2045.81535841801,299
2.51-2.70.1557.61485240671,298.9
2.7-2.970.10910.31513941801,299
2.97-3.40.071151508341941,298.5
3.4-4.270.04322.21485641841,297.9
4.27-47.3510.0425.61501144231,296

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0092refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→47.351 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 8.591 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.168
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. GLYCEROL (GOL) AND POLY ETHYLENE GLYCOL FRAGMENTS (PEG,PGE) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2115 5.1 %RANDOM
Rwork0.189 ---
obs0.191 41641 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.03 Å2 / Biso mean: 22.491 Å2 / Biso min: 6.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4634 0 50 242 4926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224804
X-RAY DIFFRACTIONr_bond_other_d0.0020.023210
X-RAY DIFFRACTIONr_angle_refined_deg1.6642.0066495
X-RAY DIFFRACTIONr_angle_other_deg0.98137899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.87124.545187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4315.241914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4761519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02898
X-RAY DIFFRACTIONr_mcbond_it1.40322906
X-RAY DIFFRACTIONr_mcbond_other0.32321201
X-RAY DIFFRACTIONr_mcangle_it2.45434677
X-RAY DIFFRACTIONr_scbond_it2.68431898
X-RAY DIFFRACTIONr_scangle_it4.30451810
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 157 -
Rwork0.239 2896 -
all-3053 -
obs--99.64 %
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)
10.09910.0282-0.00680.83990.19720.7080.00640.0219-0.02-0.00670.0285-0.01010.0281-0.0153-0.03490.0207-0.0117-0.01010.0489-0.00220.04123.282269.0183-69.3695
20.5097-0.4046-0.090.63360.13340.85840.0217-0.01380.00050.0183-0.00050.05440.05570.0075-0.02120.0445-0.0249-0.00710.03310.01240.040722.672655.3463-28.0765
30.3904-0.0524-0.38120.7963-0.65991.43520.0704-0.0064-0.01170.0521-0.06920.0171-0.1549-0.0385-0.00120.06520.00040.00220.03390.00020.03723.712281.0596-28.5776
40.0337-0.01160.10340.43090.39851.0381-0.01820.0042-0.0107-0.01230.02220.0534-0.04820.0443-0.0040.012-0.00140.00380.00540.00660.020223.793190.5443-52.2585
50.03910.168-0.32511.3799-1.11222.8394-0.03890.0082-0.0017-0.15370.02150.01520.3738-0.08770.01740.0813-0.0186-0.02580.01740.00090.044421.241748.7838-52.8621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 125
2X-RAY DIFFRACTION2B2 - 125
3X-RAY DIFFRACTION3C14 - 125
4X-RAY DIFFRACTION4D13 - 125
5X-RAY DIFFRACTION5E15 - 125

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