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- PDB-2re3: CRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SIL... -

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Basic information

Entry
Database: PDB / ID: 2re3
TitleCRYSTAL STRUCTURE OF a DUF1285 family protein (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


: / Protein of unknown function (DUF1285), C-terminal domain / duf1285 protein / duf1285 like domain / Protein of unknown function DUF1285 / DUF1285, beta-roll domain superfamily / : / Domain of unknown function (DUF1285), N-terminal domain / duf1285 like fold / duf1285 protein fold ...: / Protein of unknown function (DUF1285), C-terminal domain / duf1285 protein / duf1285 like domain / Protein of unknown function DUF1285 / DUF1285, beta-roll domain superfamily / : / Domain of unknown function (DUF1285), N-terminal domain / duf1285 like fold / duf1285 protein fold / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Single Sheet / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction.
Authors: Han, G.W. / Bakolitsa, C. / Miller, M.D. / Kumar, A. / Carlton, D. / Najmanovich, R.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, ...Authors: Han, G.W. / Bakolitsa, C. / Miller, M.D. / Kumar, A. / Carlton, D. / Najmanovich, R.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ernst, D. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Jaroszewski, L. / Jin, K.K. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 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 1.4Jan 25, 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 1.5Oct 9, 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: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3073
Polymers43,2152
Non-polymers921
Water3,351186
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7002
Polymers21,6081
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,6081
Polymers21,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.370, 75.370, 182.687
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 10 - 192 / Label seq-ID: 11 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 21607.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi DSS-3 (bacteria) / Species: Silicibacter pomeroyi / Strain: DSS-3, DSM 15171 / Gene: YP_165412.1, SPO0140 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LWU5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 20.0% Ethanol, 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: 0.91837, 0.97908, 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979081
30.979351
ReflectionResolution: 2.5→29.488 Å / Num. obs: 19038 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 4.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.567.60.7611033413570.76100
2.56-2.647.60.631.21028213480.63100
2.64-2.717.60.5211.4991413060.521100
2.71-2.87.60.4341.8961112680.434100
2.8-2.897.60.3422.2936812280.342100
2.89-2.997.50.262.9893211860.26100
2.99-3.17.60.2223.4867711440.222100
3.1-3.237.50.1654.4849811270.165100
3.23-3.377.50.1375.1803310700.137100
3.37-3.547.50.1245.2767410250.124100
3.54-3.7370.138469079860.13899.9
3.73-3.957.40.093770099410.093100
3.95-4.237.40.079.264978800.07100
4.23-4.567.40.0669.760638220.066100
4.56-57.30.0619.956297710.061100
5-5.597.20.05910.750366990.059100
5.59-6.457.10.0797.444516270.079100
6.45-7.916.90.0747.637995510.074100
7.91-11.186.60.04810.829154440.048100
11.18-29.4885.80.04212.915012580.04294.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHARPphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.488 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 15.258 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.418 / ESU R Free: 0.275
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE ELECTRON DENSITIES FOR RESIDUES 134-139 IN SUBUNIT B ARE DISORDERED, AND THESE RESIDUES WERE MODELED BASED ON THE MODEL FOR THE NCS-RELATED A SUBUNIT. 5. ONE GLYCEROL (GOL) FROM THE CRYOPROTECTION BUFFER WAS MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 972 5.1 %RANDOM
Rwork0.215 ---
obs0.217 18959 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.385 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.85 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 0 6 186 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223040
X-RAY DIFFRACTIONr_bond_other_d0.0040.022107
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.9614146
X-RAY DIFFRACTIONr_angle_other_deg0.92935089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7815389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29522.766141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0815478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4271530
X-RAY DIFFRACTIONr_chiral_restr0.0910.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
X-RAY DIFFRACTIONr_nbd_refined0.2050.2551
X-RAY DIFFRACTIONr_nbd_other0.2090.22249
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21474
X-RAY DIFFRACTIONr_nbtor_other0.0880.21670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2159
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0770.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.210
X-RAY DIFFRACTIONr_mcbond_it1.87531969
X-RAY DIFFRACTIONr_mcbond_other0.4463767
X-RAY DIFFRACTIONr_mcangle_it2.93753068
X-RAY DIFFRACTIONr_scbond_it3.51161247
X-RAY DIFFRACTIONr_scangle_it4.32261078
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2310 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.410.5
MEDIUM THERMAL0.652
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 78 -
Rwork0.28 1278 -
all-1356 -
obs--99.85 %
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)
11.14770.10530.47541.65951.08194.02910.0389-0.0431-0.0899-0.01260.092-0.19950.20170.2994-0.1309-0.0862-0.0045-0.0054-0.0501-0.0267-0.045222.55854.642146.305
21.02070.1049-1.21361.1552-0.62213.58860.1066-0.03060.20020.02-0.02260.1141-0.2148-0.107-0.084-0.098-0.02380.011-0.0387-0.0078-0.05044.279422.629139.4055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 19211 - 193
2X-RAY DIFFRACTION2BB10 - 19311 - 194

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