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- PDB-3go5: Crystal structure of a multidomain protein with nucleic acid bind... -

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Basic information

Entry
Database: PDB / ID: 3go5
TitleCrystal structure of a multidomain protein with nucleic acid binding domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 A resolution
ComponentsMultidomain protein with S1 RNA-binding domains
KeywordsGENE REGULATION / S1 rna-binding domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #330 / Conserved virulence factor B / Conserved virulence factor B, S1 domain / Conserved virulence factor B-like, winged helix domain / : / : / S1 domain / CvfB-like winged helix domain / CvfB first S1-like domain / Virulence regulatory factor CvfB, second domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #330 / Conserved virulence factor B / Conserved virulence factor B, S1 domain / Conserved virulence factor B-like, winged helix domain / : / : / S1 domain / CvfB-like winged helix domain / CvfB first S1-like domain / Virulence regulatory factor CvfB, second domain / Nucleic acid-binding proteins / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
S1 motif domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Structure / Year: 2010
Title: Structure of a virulence regulatory factor CvfB reveals a novel winged helix RNA binding module.
Authors: Matsumoto, Y. / Xu, Q. / Miyazaki, S. / Kaito, C. / Farr, C.L. / Axelrod, H.L. / Chiu, H.J. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, ...Authors: Matsumoto, Y. / Xu, Q. / Miyazaki, S. / Kaito, C. / Farr, C.L. / Axelrod, H.L. / Chiu, H.J. / Klock, H.E. / Knuth, M.W. / Miller, M.D. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Sekimizu, K. / Wilson, I.A.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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 1.4Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidomain protein with S1 RNA-binding domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54612
Polymers32,8901
Non-polymers65611
Water11,638646
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.560, 62.560, 160.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-658-

HOH

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Components

#1: Protein Multidomain protein with S1 RNA-binding domains


Mass: 32890.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: NP_345429.1, SP_0946 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q97R81, UniProt: A0A0H2UPM3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O
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.

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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: 2.75 Å3/Da / Density % sol: 55.3 %
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
Details: NANODROP, 0.3640M Ammonium dihydrogen phosphate, 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: 0.97839 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97839 Å / Relative weight: 1
ReflectionResolution: 1.4→29.136 Å / Num. obs: 72475 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 14.189 Å2 / Rmerge(I) obs: 0.085
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.4-1.450.9791.76869913414196.7
1.45-1.510.7112.57863614175199.9
1.51-1.580.5083.57821513994199.9
1.58-1.660.3644.97439413233199.9
1.66-1.760.2576.875650133841100
1.76-1.90.16310.38104014280199.9
1.9-2.090.107157779513759199.9
2.09-2.390.07719.97798713719199.9
2.39-3.010.056258033913874199.9
3.01-29.1360.04233.28071913898199.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.136 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.771 / SU ML: 0.032 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. ETHYLENE GLYCOL (EDO) AND CHLORIDE (CL) FROM THE CRYOPROTECTANT/CRYSTALLIZATION CONDITIONS ARE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 3649 5 %RANDOM
Rwork0.154 ---
obs0.155 72406 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.41 Å2 / Biso mean: 14.826 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 41 646 2977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222658
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9833605
X-RAY DIFFRACTIONr_angle_other_deg0.85734743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4624.453137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64115518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5221521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022975
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02550
X-RAY DIFFRACTIONr_mcbond_it1.24331540
X-RAY DIFFRACTIONr_mcbond_other0.3393626
X-RAY DIFFRACTIONr_mcangle_it2.1352520
X-RAY DIFFRACTIONr_scbond_it3.70781118
X-RAY DIFFRACTIONr_scangle_it5.724111053
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 251 -
Rwork0.298 4927 -
all-5178 -
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)
10.51160.40020.28191.06670.42151.5437-0.0098-0.00660.0529-0.0549-0.01190.0024-0.0995-0.02440.02170.0160.0092-0.0020.0074-0.00340.008842.847427.7831-6.845
20.4685-0.01690.2130.4367-0.03820.4310.0240.00660.0137-0.03040.0055-0.0095-0.0138-0.0196-0.02940.00690.00160.00460.00170.00250.004649.259631.899314.7732
30.7913-0.3109-0.04840.6941-0.23720.3741-0.0677-0.0549-0.05430.0420.07010.01240.0162-0.0316-0.00240.01060.00570.00490.00880.00380.004853.167315.396429.8029
40.36850.28580.01740.53070.25520.6045-0.0764-0.01230.06160.01470.04040.01950.01940.04840.0360.03660.013-0.02270.0101-0.00660.023172.6686-8.564637.6993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 63
2X-RAY DIFFRACTION2A64 - 134
3X-RAY DIFFRACTION3A135 - 216
4X-RAY DIFFRACTION4A217 - 284

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