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- PDB-2iay: Crystal structure of a duf1831 family protein (lp2179) from lacto... -

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Basic information

Entry
Database: PDB / ID: 2iay
TitleCrystal structure of a duf1831 family protein (lp2179) from lactobacillus plantarum at 1.20 A resolution
ComponentsHypothetical protein
KeywordsTRANSLATION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLp2179-like fold / Lp2179-like / Putative amino acid metabolism / Lp2179-like superfamily / Putative amino acid metabolism / 2-Layer Sandwich / Alpha Beta / Cysteine desulfurase associated protein,DUF1831 family / :
Function and homology information
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism.
Authors: Bakolitsa, C. / Kumar, A. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elsliger, M.A. / ...Authors: Bakolitsa, C. / Kumar, A. / Carlton, D. / Miller, M.D. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Grant, J.C. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Tien, H.J. / Trout, C.V. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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.pdbx_leaving_atom_flag / _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: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9993
Polymers12,8711
Non-polymers1282
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.289, 47.896, 58.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein


Mass: 12871.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: NP_785678.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88V95, UniProt: F9UQB2*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 195 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
11.9637.17THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL AND REFINED AGAINST A HIGHER RESOLUTION DATASET FROM CURRENT CRYSTAL.
2THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL AND REFINED AGAINST A HIGHER RESOLUTION DATASET FROM CURRENT CRYSTAL.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop10.50.2M NaCl, 20.0% PEG-8000, 0.1M CAPS, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 10.5
2772vapor diffusion, sitting drop, nanodrop920.0% PEG-6000, 0.1M Bicine, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 9.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.210.9798
SYNCHROTRONAPS 23-ID-D20.94926,0.97939,0.97925
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDAug 31, 2006
MARMOSAIC 300 mm CCD2CCDAug 11, 2006Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.949261
30.979391
40.979251
ReflectionResolution: 1.198→28.928 Å / Num. obs: 29115 / % possible obs: 90.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.231.40.2043.7166311650.20450.7
1.23-1.262.50.2522.9370614670.25266
1.26-1.33.10.2153.4520416810.21576.3
1.3-1.343.80.2023.6689918230.20284.3
1.34-1.394.60.1943.7889119180.19492
1.39-1.435.80.1793.91176120300.17999.4
1.43-1.496.80.1584.51336319630.15899.8
1.49-1.556.90.1355.11302818940.135100
1.55-1.626.90.1175.81253918160.11799.9
1.62-1.76.90.1116.11209117510.111100
1.7-1.796.90.16.51149716740.1100
1.79-1.96.80.0887.61087915940.088100
1.9-2.036.80.0768.21011214780.076100
2.03-2.197.20.0689.41007613900.06899.9
2.19-2.47.80.0738.51011912970.07399.9
2.4-2.6890.0748.21044611640.07499.7
2.68-3.19.80.078.71024310420.0799.3
3.1-3.799.40.05610.782858850.05699.1
3.79-5.3710.20.0491270566910.04997.9
5.37-28.929.10.05511.435783920.05595.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.2→28.928 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.142 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. A GLYCEROL MOLECULE FROM THE CRYO SOLUTION IS MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.147 1488 5.1 %RANDOM
Rwork0.12 ---
obs0.121 29080 90.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.2→28.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 6 195 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022976
X-RAY DIFFRACTIONr_bond_other_d0.0010.02656
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9711340
X-RAY DIFFRACTIONr_angle_other_deg0.99731621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10323.90241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63215176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.509156
X-RAY DIFFRACTIONr_chiral_restr0.0970.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
X-RAY DIFFRACTIONr_nbd_refined0.2170.2178
X-RAY DIFFRACTIONr_nbd_other0.1990.2680
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2483
X-RAY DIFFRACTIONr_nbtor_other0.090.2514
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.239
X-RAY DIFFRACTIONr_mcbond_it2.7273644
X-RAY DIFFRACTIONr_mcbond_other1.5193243
X-RAY DIFFRACTIONr_mcangle_it3.2115993
X-RAY DIFFRACTIONr_scbond_it4.848405
X-RAY DIFFRACTIONr_scangle_it5.67811335
X-RAY DIFFRACTIONr_rigid_bond_restr2.27531822
X-RAY DIFFRACTIONr_sphericity_free8.5693200
X-RAY DIFFRACTIONr_sphericity_bonded4.25531605
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 61 -
Rwork0.177 1093 -
obs-1154 49.13 %

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