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- PDB-3dcx: Crystal structure of a duf1696 family protein with a pleckstrin-h... -

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Entry
Database: PDB / ID: 3dcx
TitleCrystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution
ComponentsProtein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyBacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain / Bacterial Pleckstrin homology domain superfamily / Bacterial PH domain / PH-domain like / Roll / Mainly Beta / Bacterial Pleckstrin homology domain-containing protein
Function and homology information
Biological speciesShewanella loihica PV-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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
Revision 1.6Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
B: Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
C: Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
D: Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
E: Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,41113
Polymers65,5485
Non-polymers8638
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-137 kcal/mol
Surface area25350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.070, 75.320, 139.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA9 - 1242 - 117
2ALAALABB12 - 1245 - 117
3ASNASNCC10 - 1243 - 117
4ALAALADD12 - 1245 - 117
5GLUGLUEE13 - 1246 - 117
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A PENTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Protein of Unknown Function (DUF1696) with Pleckstrin-homology Domains


Mass: 13109.577 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Gene: YP_001092950.1, Shew_0819 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QB43
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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. THE CLONED CONSTRUCT CONTAINS RESIDUES 9-124 OF THE FULL LENGTH PROTEIN.

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.83
Details: 37.0% 2-methyl-2,4-pentanediol, 0.15M sodium chloride, 0.1M HEPES pH 6.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97925,0.91837,0.97871
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979251
20.918371
30.978711
ReflectionResolution: 2→29.828 Å / Num. obs: 43831 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Biso Wilson estimate: 31.07 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.19
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.6381.5168537885195.9
2.07-2.150.4692171467960197.2
2.15-2.250.3462.8181688425198
2.25-2.370.2683.5179208315197.9
2.37-2.520.2134.3180218341198.2
2.52-2.710.1466.2174738085198.3
2.71-2.990.0929.6184018508198.4
2.99-3.420.04816.5177218189198.5
3.42-4.30.02627.7178748232198.5
4.3-29.830.01937.1181278307197.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.828 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.891 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159
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. MPD AND CL ARE PRESENT IN CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2200 5 %RANDOM
Rwork0.184 ---
obs0.186 43782 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---0.94 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→29.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 57 322 4745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224619
X-RAY DIFFRACTIONr_bond_other_d0.0010.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9856282
X-RAY DIFFRACTIONr_angle_other_deg0.89537591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85125.821201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.151515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2739
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
X-RAY DIFFRACTIONr_nbd_refined0.1980.2741
X-RAY DIFFRACTIONr_nbd_other0.1940.23087
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22138
X-RAY DIFFRACTIONr_nbtor_other0.0840.22579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.221
X-RAY DIFFRACTIONr_mcbond_it1.99332977
X-RAY DIFFRACTIONr_mcbond_other0.72231164
X-RAY DIFFRACTIONr_mcangle_it2.66754611
X-RAY DIFFRACTIONr_scbond_it4.8881903
X-RAY DIFFRACTIONr_scangle_it6.697111649
Refine LS restraints NCS

Ens-ID: 1 / Number: 1157 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL1.110.5
2BMEDIUM POSITIONAL1.040.5
3CMEDIUM POSITIONAL1.190.5
4DMEDIUM POSITIONAL0.90.5
5EMEDIUM POSITIONAL0.80.5
1AMEDIUM THERMAL1.262
2BMEDIUM THERMAL1.252
3CMEDIUM THERMAL1.142
4DMEDIUM THERMAL1.162
5EMEDIUM THERMAL1.042
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 192 -
Rwork0.24 2925 -
all-3117 -
obs--96.8 %
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)
10.3303-0.0932-0.72360.76720.00541.6387-0.04750.1368-0.2331-0.0789-0.0564-0.04710.1488-0.04660.1039-0.0228-0.0201-0.0344-0.0424-0.02080.044756.6773-15.769714.207
20.4804-0.06860.17741.26140.03450.52040.0563-0.0896-0.05550.0683-0.00130.02420.0491-0.0586-0.055-0.067-0.0289-0.0248-0.05020.0157-0.090656.76796.783627.8238
30.58740.48810.07370.6305-0.09521.98090.0755-0.03690.11280.0309-0.0090.0421-0.2249-0.0239-0.0664-0.03880.01310.0205-0.0759-0.0245-0.0161.729126.761712.3471
41.39280.4912-0.46831.22760.5481.4072-0.01510.14470.0841-0.18490.10990.0386-0.10370.1016-0.0947-0.05240.0125-0.001-0.00130.0056-0.039561.09117.3352-12.2465
51.20890.41820.36151.6201-0.5873.1125-0.04330.1799-0.2502-0.2438-0.0226-0.16550.3267-0.25730.06590.0039-0.0193-0.00290.0518-0.07630.046556.4862-8.0218-9.9605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1241 - 117
2X-RAY DIFFRACTION2BB12 - 1245 - 117
3X-RAY DIFFRACTION3CC10 - 1243 - 117
4X-RAY DIFFRACTION4DD12 - 1245 - 117
5X-RAY DIFFRACTION5EE13 - 1246 - 117

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