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- PDB-1zwk: Structure of WrbA from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1zwk
TitleStructure of WrbA from Pseudomonas aeruginosa
ComponentsTrp repressor binding protein WrbA
KeywordsPROTEIN BINDING / WrbA / 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:ubiquinone reductase (non-electrogenic) activity / NAD(P)H dehydrogenase (quinone) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / FMN binding / cellular response to oxidative stress / electron transfer activity / membrane
Similarity search - Function
Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold ...Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin, conserved site / Flavodoxin signature. / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / NAD(P)H dehydrogenase (quinone)
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trp repressor binding protein WrbA
B: Trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0444
Polymers43,8542
Non-polymers1902
Water91951
1
A: Trp repressor binding protein WrbA
hetero molecules

A: Trp repressor binding protein WrbA
hetero molecules

A: Trp repressor binding protein WrbA
hetero molecules

A: Trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0888
Polymers87,7084
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10310 Å2
ΔGint-99 kcal/mol
Surface area22940 Å2
MethodPISA, PQS
2
B: Trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0222
Polymers21,9271
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Trp repressor binding protein WrbA
hetero molecules

B: Trp repressor binding protein WrbA
hetero molecules

B: Trp repressor binding protein WrbA
hetero molecules

B: Trp repressor binding protein WrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0888
Polymers87,7084
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)73.314, 73.331, 78.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number16
Space group name H-MP222
DetailsThe biological assembly is a tetramer Chain A forms a tetramer through the symmetry operators 2_555 3_556 4_556 Chain B forms a tetramer through operators 3_655 4_565 2_665

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Components

#1: Protein Trp repressor binding protein WrbA


Mass: 21926.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: wrba / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21DE3 / References: UniProt: Q9I509
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.02 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 3350, 0.12M MgCl, 0.1M Bis pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2005
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 13469 / Num. obs: 13469 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1309 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YDG

1ydg


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.518 / SU ML: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.576 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 732 5.4 %RANDOM
Rwork0.22621 ---
all0.22871 13467 --
obs0.22871 13467 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.118 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.49 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2443 0 10 51 2504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212494
X-RAY DIFFRACTIONr_bond_other_d0.0010.022340
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9883378
X-RAY DIFFRACTIONr_angle_other_deg0.77835388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.02521.97581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44215383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9721516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined0.2290.2585
X-RAY DIFFRACTIONr_nbd_other0.1770.22265
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21230
X-RAY DIFFRACTIONr_nbtor_other0.0860.21461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.25
X-RAY DIFFRACTIONr_mcbond_it0.631.51697
X-RAY DIFFRACTIONr_mcbond_other0.0831.5704
X-RAY DIFFRACTIONr_mcangle_it1.10122607
X-RAY DIFFRACTIONr_scbond_it1.1513882
X-RAY DIFFRACTIONr_scangle_it1.9414.5771
LS refinement shellResolution: 2.6→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 50 -
Rwork0.267 875 -
obs--97.16 %

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