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- PDB-5d66: Crystal structure of an ankyrin repeat domain (ABAYE2397) from Ac... -

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Basic information

Entry
Database: PDB / ID: 5d66
TitleCrystal structure of an ankyrin repeat domain (ABAYE2397) from Acinetobacter baumannii AYE at 1.00 A resolution
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown Function / ankyrin repeat domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ANK_REP_REGION domain-containing protein
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an ankyrin repeat domain (ABAYE2397) from Acinetobacter baumannii AYE at 1.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3228
Polymers43,1102
Non-polymers2136
Water13,187732
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6614
Polymers21,5551
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6614
Polymers21,5551
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.268, 43.221, 49.632
Angle α, β, γ (deg.)83.850, 89.960, 78.380
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein / ankyrin repeat domain


Mass: 21554.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AYE) (bacteria)
Strain: AYE / Gene: ABAYE2397 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B0VB33
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium chloride, 20.0% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 9, 2014
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1→27.228 Å / Num. all: 156154 / Num. obs: 156154 / % possible obs: 82.5 % / Redundancy: 4 % / Rpim(I) all: 0.045 / Rrim(I) all: 0.089 / Rsym value: 0.077 / Net I/av σ(I): 5.264 / Net I/σ(I): 9.4 / Num. measured all: 618768
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1-1.033.90.8290.71611601140810.4170.8290.71611.929.1
1.03-1.053.90.6040.5221.42334459390.3040.6040.5222.443.3
1.05-1.083.90.4330.37423318784450.2180.4330.3743.263.8
1.08-1.1240.3260.2822.645420114480.1640.3260.2824.188.9
1.12-1.1540.2480.2143.444782112540.1240.2480.2145.189.8
1.15-1.240.2090.181443538109360.1050.2090.1815.990.6
1.2-1.2440.1840.1594.542407106500.0920.1840.1596.791.2
1.24-1.2940.1640.1424.940755102260.0820.1640.1427.391.8
1.29-1.3540.1530.1335.13971799840.0770.1530.1337.992.3
1.35-1.4140.1350.1175.83799195330.0670.1350.1178.893.1
1.41-1.4940.1190.1036.43668692110.060.1190.1031093.6
1.49-1.5840.1050.0917.23455286790.0530.1050.09111.494.3
1.58-1.6940.0960.0837.83285882490.0480.0960.08312.695
1.69-1.8340.0880.0768.63096477760.0440.0880.07613.995.6
1.83-23.90.0810.078.92796870990.0410.0810.0715.995.7
2-2.2440.0730.0639.62538764260.0370.0730.06317.496
2.24-2.583.90.0710.0629.92233157100.0360.0710.06218.195.8
2.58-3.1640.0660.05710.61946549090.0330.0660.0571997.9
3.16-4.473.80.0590.05111.81407436650.0310.0590.05119.794.8
4.47-27.2283.80.070.0610.2733119340.0370.070.0618.891.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALA3.3.20data scaling
SHELXphasing
SHARPphasing
REFMAC5.8.0103refinement
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1→27.228 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 0.852 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 7870 5 %RANDOM
Rwork0.139 148222 --
obs0.1404 156092 82.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.55 Å2 / Biso mean: 12.2327 Å2 / Biso min: 4.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20.36 Å2-0.11 Å2
2--0.5 Å2-0.01 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1→27.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 6 732 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223282
X-RAY DIFFRACTIONr_bond_other_d0.0020.023287
X-RAY DIFFRACTIONr_angle_refined_deg1.671.9624499
X-RAY DIFFRACTIONr_angle_other_deg1.04637540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63724.61141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78115588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5441522
X-RAY DIFFRACTIONr_chiral_restr0.1180.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023915
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02749
X-RAY DIFFRACTIONr_mcbond_it0.9230.7611698
X-RAY DIFFRACTIONr_mcbond_other0.9220.761697
X-RAY DIFFRACTIONr_mcangle_it1.121.1492163
X-RAY DIFFRACTIONr_rigid_bond_restr2.78536569
X-RAY DIFFRACTIONr_sphericity_free25.9445427
X-RAY DIFFRACTIONr_sphericity_bonded7.45656832
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 207 -
Rwork0.325 3871 -
all-4078 -
obs--29.09 %

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