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- PDB-1ydg: Crystal Structure of Trp repressor binding protein WrbA -

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Basic information

Entry
Database: PDB / ID: 1ydg
TitleCrystal Structure of Trp repressor binding protein WrbA
Componentstrp repressor binding protein WrbA
KeywordsPROTEIN BINDING / tetramer / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) / NADPH dehydrogenase (quinone) activity / NADH dehydrogenase (quinone) (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / FMN binding / membrane
Similarity search - Function
Flavoprotein WrbA-like / Flavodoxin domain / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.
Authors: Gorman, J. / Shapiro, L.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: trp repressor binding protein WrbA
B: trp repressor binding protein WrbA
C: trp repressor binding protein WrbA
D: trp repressor binding protein WrbA
E: trp repressor binding protein WrbA
F: trp repressor binding protein WrbA
G: trp repressor binding protein WrbA
H: trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,91518
Polymers180,9558
Non-polymers96110
Water23,2931293
1
A: trp repressor binding protein WrbA
B: trp repressor binding protein WrbA
C: trp repressor binding protein WrbA
D: trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9589
Polymers90,4774
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-157 kcal/mol
Surface area28310 Å2
MethodPISA
2
E: trp repressor binding protein WrbA
F: trp repressor binding protein WrbA
G: trp repressor binding protein WrbA
H: trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9589
Polymers90,4774
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-156 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.611, 121.611, 207.933
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is a tetramer, there are two in the asymmetric unit. 1: Chains A, B, C, D 2: Chains E, F, G, H

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Components

#1: Protein
trp repressor binding protein WrbA


Mass: 22619.314 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DRA0214 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9RYU4
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1293 / 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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 2.6M AmSulfate, 20% Glycerol, pH 4.5, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
127.7 mg/mlprotein1drop
210 mMHEPES1droppH7.5
3150 mM1dropNaCl
410 %glycerol1drop
52.6 Mammonium sulfate1reservoir
620 %glycerol1reservoir
75 mMdithiothreitol1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 2003
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 120346 / Num. obs: 116736 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.6 / Num. unique all: 11858 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 97 %
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.89 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.186 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23551 5845 5 %RANDOM
Rwork0.18632 ---
all0.18877 116506 --
obs0.18877 116506 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.254 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.12 Å20 Å2
2--0.25 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12056 0 50 1293 13399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211075
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.95316771
X-RAY DIFFRACTIONr_angle_other_deg0.767325735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86951608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.6124.531512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83151945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.581572
X-RAY DIFFRACTIONr_chiral_restr0.0620.21879
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214008
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022416
X-RAY DIFFRACTIONr_nbd_refined0.20.22869
X-RAY DIFFRACTIONr_nbd_other0.1810.210961
X-RAY DIFFRACTIONr_nbtor_refined0.1730.26138
X-RAY DIFFRACTIONr_nbtor_other0.0840.26415
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.21087
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0870.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.231
X-RAY DIFFRACTIONr_mcbond_it1.0531.510262
X-RAY DIFFRACTIONr_mcbond_other0.1281.53336
X-RAY DIFFRACTIONr_mcangle_it1.155212726
X-RAY DIFFRACTIONr_scbond_it1.54635070
X-RAY DIFFRACTIONr_scangle_it2.3764.54045
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 436 -
Rwork0.232 8192 -
obs-8192 99.37 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.25 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.182
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å

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