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- PDB-1yrh: Crystal Structure Of Trp Repressor Binding Protein Wrba in comple... -

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Basic information

Entry
Database: PDB / ID: 1yrh
TitleCrystal Structure Of Trp Repressor Binding Protein Wrba in complex with FMN
Componentstrp repressor binding protein WrbA
KeywordsPROTEIN BINDING / alpha-beta twisted open sheet / 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
FLAVIN MONONUCLEOTIDE / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.11 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
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)186,85616
Polymers183,2058
Non-polymers3,6518
Water2,900161
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)93,4288
Polymers91,6034
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-95 kcal/mol
Surface area27210 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)93,4288
Polymers91,6034
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-95 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.327, 122.327, 208.735
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer. There are two in the asymmetric unit: A, B, C, D form one biological unit and E, F, G, H form a second

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Components

#1: Protein
trp repressor binding protein WrbA


Mass: 22900.686 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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 2.6M AMSULFATE, 20% GLYCEROL, pH 4.5, VAPOR DIFFUSION, temperature 293K

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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: Aug 9, 2004
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. all: 32107 / Num. obs: 32107 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.6
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3169 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: SAD / Resolution: 3.11→20 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.868 / SU B: 16.514 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1632 5.1 %RANDOM
Rwork0.1978 ---
all0.19954 32058 --
obs0.19954 32055 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 3.11→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11977 0 248 161 12386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211131
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.97116981
X-RAY DIFFRACTIONr_angle_other_deg0.871325861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.851595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.11724.531512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.036151936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5141572
X-RAY DIFFRACTIONr_chiral_restr0.0560.21885
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022407
X-RAY DIFFRACTIONr_nbd_refined0.2010.23082
X-RAY DIFFRACTIONr_nbd_other0.180.211424
X-RAY DIFFRACTIONr_nbtor_refined0.1810.26205
X-RAY DIFFRACTIONr_nbtor_other0.080.26886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.28
X-RAY DIFFRACTIONr_mcbond_it0.5151.59672
X-RAY DIFFRACTIONr_mcbond_other0.0561.53309
X-RAY DIFFRACTIONr_mcangle_it0.56212604
X-RAY DIFFRACTIONr_scbond_it0.98635432
X-RAY DIFFRACTIONr_scangle_it1.5284.54377
LS refinement shellResolution: 3.11→3.189 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 124 -
Rwork0.23 2135 -
obs--95.96 %

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