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- PDB-4rgl: Crystal structure of a Fic family protein (Dde_2494) from Desulfo... -

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Basic information

Entry
Database: PDB / ID: 4rgl
TitleCrystal structure of a Fic family protein (Dde_2494) from Desulfovibrio desulfuricans G20 at 2.70 A resolution
ComponentsFilamentation induced by cAMP protein Fic
KeywordsDNA BINDING PROTEIN / PF02661 family / Fic/DOC protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyFido domain-containing protein / Fido-like domain superfamily / Fido domain / Fic/DOC family / Fido domain profile. / Winged helix DNA-binding domain superfamily / Unknown ligand / Filamentation induced by cAMP protein Fic
Function and homology information
Biological speciesDesulfovibrio alaskensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Fic family protein (Dde_2494) from Desulfovibrio desulfuricans G20 at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Filamentation induced by cAMP protein Fic


Theoretical massNumber of molelcules
Total (without water)39,3002
Polymers39,3001
Non-polymers01
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.129, 56.129, 251.447
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 Filamentation induced by cAMP protein Fic


Mass: 39299.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: Dde_2494 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q30YF5
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (1-342) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-342) 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 40.0% MPD, 0.1M CAPS pH 10.5, NANODROP, 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: 0.97895,0.97929,0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2007
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.979291
30.918371
ReflectionResolution: 2.7→41.908 Å / Num. obs: 11879 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.83 % / Biso Wilson estimate: 79.008 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.86.881.2611.77724112394.8
2.8-2.910.8312.679871125100
2.91-3.040.5843.680071129100
3.04-3.20.3645.382921168100
3.2-3.40.227.882271171100
3.4-3.660.14411.180351168100
3.66-4.030.08616.68198120299.8
4.03-4.60.05823.181421179100
4.6-5.770.053268229123099.9
5.77-41.910.04530.48287138498.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→41.908 Å / Cor.coef. Fo:Fc: 0.9201 / Cor.coef. Fo:Fc free: 0.8767 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.4. VAL 33 IS IN A REGIONS OF POOR ELECTRON DENSITY AND IS RAMACHANDRAN OUTLIER IN MOLPROBITY. 5.ELECTRON DENSITY CORRESPONDING TO AN INTER-DOMAIN LINKER BETWEEN THR 257-GLN 263 IS DISORDERED AND THIS REGION COULD NOT BE RELIABLY MODELED.THE POSITIONING OF THE TWO DOMAINS FROM A SINGLE SUBUNIT IS BASED ON THE PROXIMITY OF THE C-TERMINAL END OF ONE DOMAIN TO THE N-TERMINAL END OF THE SECOND DOMAIN. 6. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE PUTATIVE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 560 4.74 %RANDOM
Rwork0.2274 ---
obs0.229 11803 99.38 %-
Displacement parametersBiso max: 180.99 Å2 / Biso mean: 91.267 Å2 / Biso min: 36.93 Å2
Baniso -1Baniso -2Baniso -3
1--10.6196 Å20 Å20 Å2
2---10.6196 Å20 Å2
3---21.2392 Å2
Refine analyzeLuzzati coordinate error obs: 0.495 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 18 20 2584
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1201SINUSOIDAL12
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes383HARMONIC5
X-RAY DIFFRACTIONt_it2598HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion342SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3174SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2598HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg3536HARMONIC80.38
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion1.95
LS refinement shellResolution: 2.7→2.96 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2897 132 4.89 %
Rwork0.2552 2567 -
all0.2568 2699 -
obs--99.38 %
Refinement TLS params.Method: refined / Origin x: -5.2389 Å / Origin y: 19.9229 Å / Origin z: 44.625 Å
111213212223313233
T0.0533 Å2-0.0609 Å20.0152 Å2-0.1234 Å20.0283 Å2---0.0145 Å2
L2.3245 °2-1.6362 °2-0.4303 °2-1.4741 °2-0.076 °2--1.2082 °2
S-0.2768 Å °-0.0984 Å °-0.1149 Å °0.1785 Å °0.2253 Å °0.14 Å °0.0218 Å °-0.1217 Å °0.0515 Å °
Refinement TLS groupSelection details: { A|7-334 }

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