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- PDB-3pjy: Crystal structure of a putative transcription regulator (R01717) ... -

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Basic information

Entry
Database: PDB / ID: 3pjy
TitleCrystal structure of a putative transcription regulator (R01717) from Sinorhizobium meliloti 1021 at 1.55 A resolution
ComponentsHypothetical signal peptide protein
KeywordsTRANSCRIPTION REGULATOR / DUF192 FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF192 / Protein of unknown function DUF192 / Saro_0823-like superfamily / Uncharacterized ACR, COG1430 / Jelly Rolls / Sandwich / Mainly Beta / Hypothetical signal peptide protein
Function and homology information
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative transcription regulator (R01717) from Sinorhizobium meliloti 1021 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Feb 1, 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
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical signal peptide protein
B: Hypothetical signal peptide protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3027
Polymers30,9432
Non-polymers3595
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.435, 63.435, 153.938
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 Hypothetical signal peptide protein


Mass: 15471.558 Da / Num. of mol.: 2 / Fragment: sequence database residues 29-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: R01717, SMc00288 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q92PM3
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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 29-163 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: 2.5 Å3/Da / Density % sol: 50.85 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.20M (NH4)2SO4, 10.00% Glycerol, 20.00% PEG-300, 0.1M Phosphate Citrate pH 4.2, NANODROP, 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: 0.91162,0.97980,0.97961
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 5, 2010 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.97981
30.979611
ReflectionResolution: 1.55→29.208 Å / Num. obs: 45713 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.797 % / Biso Wilson estimate: 20.821 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.55-1.610.5761.7227679108197.2
1.61-1.670.4152.3202328035199.5
1.67-1.750.3053.1229929060199.4
1.75-1.840.1934.9213278383199.2
1.84-1.950.1317.1210848198198.4
1.95-2.10.08311.1221628526197.5
2.1-2.310.05715.8220328345195.9
2.31-2.650.04221227058427194.3
2.65-3.330.02830.4218777908191.3
3.33-29.2080.0242.7220817748187.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.208 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.381 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.073
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SULPHATE AND CHLORIDE IONS FROM THE CRYSTALLIZATION AND PROTEIN BUFFERS ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2298 5 %RANDOM
Rwork0.1611 ---
obs0.1626 45642 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73 Å2 / Biso mean: 24.0432 Å2 / Biso min: 11.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 17 278 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212294
X-RAY DIFFRACTIONr_bond_other_d0.0010.021571
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9843136
X-RAY DIFFRACTIONr_angle_other_deg0.90933823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9725302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63122.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58615400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4791524
X-RAY DIFFRACTIONr_chiral_restr0.0960.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212652
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02470
X-RAY DIFFRACTIONr_mcbond_it1.67631434
X-RAY DIFFRACTIONr_mcbond_other0.4913576
X-RAY DIFFRACTIONr_mcangle_it2.67252339
X-RAY DIFFRACTIONr_scbond_it4.3548860
X-RAY DIFFRACTIONr_scangle_it6.79411797
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 159 -
Rwork0.282 3143 -
all-3302 -
obs--98.33 %
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)
10.96360.08970.14091.4-0.47661.0002-0.021-0.0601-0.03430.08660.00840.05870.023-0.06760.01260.0431-0.0170.0110.05160.03210.04381.938521.244233.939
21.588-0.382-0.30520.98070.05020.84340.0301-0.00590.03350.09440.01170.0352-0.0386-0.0198-0.04180.0520.00280.02560.0033-0.00160.025117.32497.979159.2087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 156
2X-RAY DIFFRACTION2B0 - 157

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