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- PDB-2qtp: Crystal structure of a duf1185 family protein (spo0826) from sili... -

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Basic information

Entry
Database: PDB / ID: 2qtp
TitleCrystal structure of a duf1185 family protein (spo0826) from silicibacter pomeroyi dss-3 at 2.10 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyBB2672 / Amino acid synthesis, putative / BB2672 superfamily / Amino acid synthesis / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesSilicibacter pomeroyi DSS-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.
Authors: Bakolitsa, C. / Kumar, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chen, C. / Chiu, H. ...Authors: Bakolitsa, C. / Kumar, A. / Jin, K.K. / McMullan, D. / Krishna, S.S. / Miller, M.D. / Abdubek, P. / Acosta, C. / Astakhova, T. / Axelrod, H.L. / Burra, P. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Elias, Y. / Ellrott, K. / Ernst, D. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Johnson, H.A. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Marciano, D. / Morse, A.T. / Murphy, K.D. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Paulsen, J. / Puckett, C. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Tien, H.J. / Trame, C.B. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionAug 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Oct 25, 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 1.5Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)20,8121
Polymers20,8121
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein

A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,6242
Polymers41,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.730, 94.730, 47.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uncharacterized protein


Mass: 20812.057 Da / Num. of mol.: 1
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_166079.1, SPO0826 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LV76
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.1M Sodium dihydrogen phosphate, 0.1M Potassium dihydrogen phosphate, 2.0M Sodium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97922, 0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979221
30.979051
ReflectionResolution: 2.1→27.308 Å / Num. obs: 13007 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.74 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 15.82
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.717282712199198.2
2.17-2.260.5082.996012500199.8
2.26-2.360.3963.790482356199.8
2.36-2.490.3114.696322507199.9
2.49-2.640.2216.7889323171100
2.64-2.850.13510.3942624621100
2.85-3.130.0741790472354199.9
3.13-3.590.03827.192962423199.7
3.59-4.510.0243990042362199.3
4.51-27.3080.02245.288802361196.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→27.308 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.222 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.168
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. RESIDUES 0 TO 2, 103 TO 115, 137 TO 145, 171 TO 193 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 631 4.9 %RANDOM
Rwork0.204 ---
obs0.207 12970 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 0 42 1118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221120
X-RAY DIFFRACTIONr_bond_other_d0.0010.02755
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9861519
X-RAY DIFFRACTIONr_angle_other_deg0.92531856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5275150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12624.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74515189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.623159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
X-RAY DIFFRACTIONr_nbd_refined0.2080.3179
X-RAY DIFFRACTIONr_nbd_other0.2010.3724
X-RAY DIFFRACTIONr_nbtor_refined0.1680.5525
X-RAY DIFFRACTIONr_nbtor_other0.0940.5603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.560
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3590.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.58
X-RAY DIFFRACTIONr_mcbond_it2.1663769
X-RAY DIFFRACTIONr_mcbond_other0.4893303
X-RAY DIFFRACTIONr_mcangle_it3.49951195
X-RAY DIFFRACTIONr_scbond_it6.298388
X-RAY DIFFRACTIONr_scangle_it8.88811324
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 53 -
Rwork0.293 882 -
obs-935 98.32 %
Refinement TLS params.Method: refined / Origin x: 54.534 Å / Origin y: 23.346 Å / Origin z: 10.278 Å
111213212223313233
T-0.3326 Å2-0.0415 Å2-0.0417 Å2--0.2806 Å20.0336 Å2---0.1998 Å2
L3.319 °22.6145 °2-1.1479 °2-4.8026 °2-1.924 °2--2.3208 °2
S-0.1504 Å °0.3481 Å °0.3173 Å °-0.2503 Å °0.1718 Å °0.2502 Å °-0.138 Å °0.0642 Å °-0.0214 Å °

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