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- PDB-2q3l: CRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3478 FAMI... -

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Database: PDB / ID: 2q3l
TitleCRYSTAL STRUCTURE OF AN UNCHARACTERIZED PROTEIN FROM DUF3478 FAMILY WITH A SPOIIAA-LIKE FOLD (SHEW_3102) FROM SHEWANELLA LOIHICA PV-4 AT 2.25 A RESOLUTION
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SPOIIAA-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologySpoIIaa-like domains / SpoIIAA-like / SpoIIAA-like superfamily / SpoIIAA-like / STAS domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / STAS/SEC14 domain-containing protein
Function and homology information
Biological speciesShewanella loihica PV-4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Open and closed conformations of two SpoIIAA-like proteins (YP_749275.1 and YP_001095227.1) provide insights into membrane association and ligand binding.
Authors: Kumar, A. / Lomize, A. / Jin, K.K. / Carlton, D. / Miller, M.D. / Jaroszewski, L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. ...Authors: Kumar, A. / Lomize, A. / Jin, K.K. / Carlton, D. / Miller, M.D. / Jaroszewski, L. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / 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
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 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 1.6Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 20, 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 600 HETEROGEN THE MPD USED AS A CRYOPROTECTANT WAS A RACEMIC MIXTURE: (4R,S)-2-METHYL-2,4-PENTANEDIOL
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 (0) 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)29,72815
Polymers28,5482
Non-polymers1,18013
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-168 kcal/mol
Surface area13520 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,72815
Polymers28,5482
Non-polymers1,18013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area5470 Å2
ΔGint-174 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.387, 113.963, 130.692
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEILEILEAA1 - 482 - 49
21MSEMSEILEILEBB1 - 482 - 49
32ILEILECYSCYSAA53 - 12554 - 126
42ILEILECYSCYSBB53 - 12554 - 126
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 14273.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica PV-4 (bacteria) / Species: Shewanella loihica / Strain: BAA-1088, PV-4 / Gene: YP_001095227.1, Shew_3102 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A3QHM0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.33
Details: NANODROP, 0.2M Sodium chloride, 37.0% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.33, 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, 0.97926, 0.97895
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 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
20.979261
30.978951
ReflectionResolution: 2.25→28.653 Å / Num. obs: 14575 / % possible obs: 99 % / Redundancy: 7.2 % / Biso Wilson estimate: 41.73 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.3170.4673.6744510600.467100
2.31-2.377.10.3951.9719210110.39597.1
2.37-2.447.20.3432.271889980.34399.7
2.44-2.527.20.2762.871729910.27698.1
2.52-2.67.30.2483.168279310.24899.4
2.6-2.697.30.1844.166969170.18497.9
2.69-2.797.30.1455.164608800.14599.8
2.79-2.97.30.1325.662918590.13298
2.9-3.037.30.116.260628290.11100
3.03-3.187.30.0868.157797920.08698.3
3.18-3.357.20.0689.555317690.06899.1
3.35-3.567.30.0581151116980.05899.6
3.56-3.87.20.05112.748706750.05198.7
3.8-4.117.10.04513.644686280.04599.2
4.11-4.57.10.03916.841955890.03999.4
4.5-5.0370.03616.738285430.03699.7
5.03-5.8170.04314.833044720.04399.2
5.81-7.126.90.04913.127824060.04999.7
7.12-10.066.60.04215.522243390.04299.7
10.06-28.65360.0331911211880.03395.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→28.653 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.875 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.216
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. SODIUM IONS, CHLORIDE IONS AND 2-METHYL-2,4-PENTANEDIOL (MPD) MOLECULES FROM CRYSTALIZATION ARE MODELED IN THE STRUCTURE. 5. ONE GLYCINE FROM PROTEIN EXPRESSION TAG AT N-TERMINAL IS ALSO BUILT IN EACH SUBUNIT. 6. RESIDUES 49 TO 52 IN SUBUNIT B ARE DISORDERED AND NOT BUILT IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 754 5.2 %RANDOM
Rwork0.181 ---
obs0.184 14570 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.526 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2--0.8 Å20 Å2
3----4.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→28.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1937 0 76 95 2108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222072
X-RAY DIFFRACTIONr_bond_other_d0.0020.021921
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9842811
X-RAY DIFFRACTIONr_angle_other_deg0.87134435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.095251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89224.94591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.08156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_nbd_refined0.220.3351
X-RAY DIFFRACTIONr_nbd_other0.1580.31766
X-RAY DIFFRACTIONr_nbtor_refined0.1790.5957
X-RAY DIFFRACTIONr_nbtor_other0.090.51257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.5161
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.512
X-RAY DIFFRACTIONr_mcbond_it1.68431240
X-RAY DIFFRACTIONr_mcbond_other0.6053523
X-RAY DIFFRACTIONr_mcangle_it2.84551966
X-RAY DIFFRACTIONr_scbond_it5.7038870
X-RAY DIFFRACTIONr_scangle_it7.99511845
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1757 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.490.5
MEDIUM THERMAL1.022
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 66 -
Rwork0.211 978 -
obs-1044 100 %
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)
11.68280.1788-0.79761.2981-0.48573.14540.1918-0.11250.1562-0.17570.0460.0522-0.2576-0.3586-0.2378-0.15370.040.0405-0.10310.0398-0.219415.381736.646418.2523
23.3034-0.4848-1.67161.91221.20253.43590.33040.28840.578-0.10690.0455-0.1467-0.73660.0772-0.37590.0633-0.00980.128-0.17430.1039-0.110340.258946.206-8.2448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1251 - 126
2X-RAY DIFFRACTION2BB0 - 1251 - 126

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