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- PDB-3u0i: Crystal Structure of a probable FAD-binding, putative uncharacter... -

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Basic information

Entry
Database: PDB / ID: 3u0i
TitleCrystal Structure of a probable FAD-binding, putative uncharacterized protein from Brucella melitensis
Componentsprobable FAD-binding, putative uncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Emerald BioStructures / Structural Genomics / 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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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
Authors: Seattle Structural Genomics Center for Infectious Disease / Gardberg, A. / Abendroth, J. / Fox, D. / Staker, B. / Stewart, L.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 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

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Assembly

Deposited unit
A: probable FAD-binding, putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4003
Polymers17,1301
Non-polymers2692
Water1,15364
1
A: probable FAD-binding, putative uncharacterized protein
hetero molecules

A: probable FAD-binding, putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8006
Polymers34,2612
Non-polymers5394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3720 Å2
ΔGint5 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.970, 77.970, 63.380
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 probable FAD-binding, putative uncharacterized protein


Mass: 17130.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (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-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 9.5
Details: Internal tracking number 222033a7. JCSG screen condition A7: 20% PEG8000, 0.1 M CHES, BrabA.17620.a.A1 PS01056 at 40.2mg/ml, pH 9.5, vapor diffusion, sitting drop, temperature 290K

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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: 2.2→46.21 Å / Num. obs: 21490 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 43.329 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 23.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.261.80.332.82575139886.3
2.26-2.320.3752.83177146692.4
2.32-2.390.2564.43982150798.6
2.39-2.460.2635.25178148799.3
2.46-2.540.2136.85507144099.7
2.54-2.630.1618.75402141199.7
2.63-2.730.12310.95092132899.7
2.73-2.840.10212.64945127999.8
2.84-2.970.07616.14862125899.9
2.97-3.110.06218.84706120599.9
3.11-3.280.04624.64296110699.9
3.28-3.480.03334.44227109499.9
3.48-3.720.02743.43945101299.8
3.72-4.020.02152.7364093299.6
4.02-4.40.01862.2328884398.9
4.4-4.920.01668.23033781100
4.92-5.680.01863.6263267099.6
5.68-6.960.019592285580100
6.96-9.840.01475.6180646099.6
9.84-46.210.01487.690123397.1

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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 2HQ9

2hq9


Resolution: 2.2→46.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.486 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 549 4.8 %RANDOM
Rwork0.19 ---
obs0.191 11534 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.702 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 17 64 1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191042
X-RAY DIFFRACTIONr_bond_other_d0.0030.02723
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9481409
X-RAY DIFFRACTIONr_angle_other_deg0.84931734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17522.45353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48615169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1241512
X-RAY DIFFRACTIONr_chiral_restr0.0870.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 31 -
Rwork0.25 690 -
all-721 -
obs--91.73 %
Refinement TLS params.Method: refined / Origin x: 2.362 Å / Origin y: 56.809 Å / Origin z: 8.039 Å
111213212223313233
T0.049 Å20.0012 Å2-0.0031 Å2-0.0348 Å20.0078 Å2--0.0204 Å2
L2.0095 °20.2283 °20.253 °2-3.4569 °20.6611 °2--1.601 °2
S-0.0396 Å °0.0923 Å °-0.0771 Å °-0.0942 Å °0.1428 Å °0.0984 Å °0.0559 Å °-0.0695 Å °-0.1032 Å °

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