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- PDB-3u5w: Crystal Structure of a probable FAD-binding, putative uncharacter... -

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Basic information

Entry
Database: PDB / ID: 3u5w
TitleCrystal Structure of a probable FAD-binding, putative uncharacterized protein from Brucella melitensis, apo form
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Seattle Structural Genomics Center for Infectious Disease / FMN-BINDING PROTEIN
Function / homologyPyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Pyridoxamine 5'-phosphate oxidase family protein
Function and homology information
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of a probable FAD-binding, putative uncharacterized protein from Brucella melitensis, apo form
Authors: Seattle Structural Genomics Center for Infectious Disease / Gardberg, A. / Abendroth, J. / Fox III, D. / Staker, B. / Stewart, L.
History
DepositionOct 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2634
Polymers17,1301
Non-polymers1333
Water86548
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5278
Polymers34,2612
Non-polymers2666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2690 Å2
ΔGint-55 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.180, 77.180, 63.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative uncharacterized protein


Mass: 17130.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: BAB1_1392 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YQN9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.32 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Internal tracking number 222033C10. JCSG screen condition C10: 10% PEG8000, 2% (v/v) dioxane, 0.1 M Bicine, BrabA.17620.a.A1 PS01056 at 40.2mg/ml, vapor diffusion, sitting drop, temperature ...Details: Internal tracking number 222033C10. JCSG screen condition C10: 10% PEG8000, 2% (v/v) dioxane, 0.1 M Bicine, BrabA.17620.a.A1 PS01056 at 40.2mg/ml, vapor diffusion, sitting drop, temperature 290K, pH 9.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 13680 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 42.843 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.95
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.14.80.5063.2419787485.4
2.1-2.160.464.2543296695.5
2.16-2.220.3526669795999.5
2.22-2.290.3436640191298.1
2.29-2.370.3036.8634489898.4
2.37-2.450.2528.1624387697.7
2.45-2.540.2069.7592583898.4
2.54-2.650.15312.1580681797
2.65-2.760.12314.4559278097.9
2.76-2.90.10716.2522673598.3
2.9-3.060.08120.4498870196.7
3.06-3.240.06524.9491668398.1
3.24-3.470.04735.1455563699.5
3.47-3.740.03744.4420860499.7
3.74-4.10.03150.5387656199.1
4.1-4.580.02857.5347050198.4
4.58-5.290.02856.7318446099.1
5.29-6.480.02754.5270338899.5
6.48-9.170.02359.72067306100
9.17-500.01760.6112018598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3UOI

3uoi


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.47 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 664 4.9 %RANDOM
Rwork0.211 ---
obs0.212 13679 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 6 48 1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191033
X-RAY DIFFRACTIONr_bond_other_d0.0010.02704
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9381396
X-RAY DIFFRACTIONr_angle_other_deg0.79931695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44623.07752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96615173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6971510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021156
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 42 -
Rwork0.245 773 -
all-815 -
obs--84.54 %
Refinement TLS params.Method: refined / Origin x: 36.44 Å / Origin y: -10.844 Å / Origin z: 13.075 Å
111213212223313233
T0.1077 Å20.0031 Å20.0139 Å2-0.039 Å2-0.0083 Å2--0.0337 Å2
L2.4382 °2-0.2324 °20.0183 °2-3.4923 °2-0.9884 °2--2.3183 °2
S-0.0846 Å °-0.1593 Å °-0.0057 Å °0.001 Å °0.1946 Å °-0.0593 Å °0.0273 Å °0.127 Å °-0.1099 Å °

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