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- PDB-7kb2: Putative ankyrin repeat domain-containing protein from Enterobact... -

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Basic information

Entry
Database: PDB / ID: 7kb2
TitlePutative ankyrin repeat domain-containing protein from Enterobacter cloacae
ComponentsANK_REP_REGION domain-containing protein
KeywordsPROTEIN BINDING / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / ankyrin repeat
Function / homology
Function and homology information


: / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesEnterobacter cloacae subsp. cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsOsipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Putative ankyrin repeat domain-containing protein from Enterobacter cloacae
Authors: Osipiuk, J. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANK_REP_REGION domain-containing protein
B: ANK_REP_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3456
Polymers39,9232
Non-polymers4214
Water5,044280
1
A: ANK_REP_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3214
Polymers19,9621
Non-polymers3593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANK_REP_REGION domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0242
Polymers19,9621
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.587, 56.354, 106.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANK_REP_REGION domain-containing protein


Mass: 19961.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae subsp. cloacae (strain ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56) (bacteria)
Strain: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56 / Gene: ECL_01554 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3CKN4
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M sodium acetate, 0.1 M MES:NaOH, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41876 / % possible obs: 99.4 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.04 / Rrim(I) all: 0.134 / Χ2: 1.9 / Net I/av σ(I): 27.1 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.635.91.0711.7520360.5820.4731.1740.53899.4
1.63-1.6660.88720800.5650.3890.9710.62799.3
1.66-1.696.10.81920480.6260.3570.8950.66799.2
1.69-1.726.20.76820510.6950.3320.8380.75899.2
1.72-1.766.20.67720740.7680.2890.7380.85599.1
1.76-1.85.90.58120420.7510.2570.6370.97498.9
1.8-1.856.20.49820420.820.2150.5441.14999
1.85-1.96.60.43220900.8390.1810.4691.2499.5
1.9-1.956.60.36320650.9180.1530.3951.5799.4
1.95-2.026.50.30520990.9410.1290.3321.82999.2
2.02-2.096.30.26420470.9530.1140.2882.07798.9
2.09-2.177.20.24820530.9570.0970.2682.09798.5
2.17-2.278.40.22820870.9710.0820.2432.13899.2
2.27-2.399.40.20920980.9750.0710.2212.135100
2.39-2.5411.20.220980.9820.0610.2092.245100
2.54-2.7412.10.18121180.9880.0540.192.31599.9
2.74-3.0111.90.15421220.9890.0460.1612.4100
3.01-3.4512.40.12621510.9930.0370.1322.505100
3.45-4.3411.50.11121720.9930.0340.1162.55199.9
4.34-5011.10.09723030.9950.030.1022.855100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→49.82 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.826 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 2062 4.9 %RANDOM
Rwork0.1798 ---
obs0.1821 39753 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.05 Å2 / Biso mean: 29.263 Å2 / Biso min: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--1.32 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 1.6→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2747 0 28 280 3055
Biso mean--38.78 38.77 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132867
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172716
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6483890
X-RAY DIFFRACTIONr_angle_other_deg1.4861.5796354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.19425.547137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.421159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
LS refinement shellResolution: 1.604→1.645 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 137 -
Rwork0.256 2851 -
all-2988 -
obs--97.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16650.26380.26530.54050.55510.57120.01920.0033-0.01480.0307-0.0176-0.00560.0319-0.018-0.00160.00660.00560.01040.01020.01130.039947.800848.113815.6655
21.14-0.19670.76960.14-0.09840.550.0298-0.1203-0.11820.03240.01710.02190.0385-0.0914-0.04690.0164-0.00790.0090.0168-0.00160.06332.492746.901142.0722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 503
2X-RAY DIFFRACTION2B26 - 501

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