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- PDB-4ev1: Anabaena Tic22 (protein transport) -

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Basic information

Entry
Database: PDB / ID: 4ev1
TitleAnabaena Tic22 (protein transport)
ComponentsAnabena Tic22
KeywordsCHAPERONE / Tic22 fold / chaperon / protein transport / Tic22-like family / Thylakoids
Function / homologyTic22-like / Tic22-like family / chloroplast / protein transport / Alr0114 protein
Function and homology information
Biological speciesAnabaena sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsKoenig, P. / Schleiff, E. / Sinning, I. / Tews, I.
CitationJournal: TO BE PUBLISHED
Title: Functional conservation of Tic22 in cyanobacterial outer membrane protein assembly and chloroplast translocation.
Authors: Tripp, J. / Hahn, A. / Koenig, P. / Flinner, N. / Bublak, D. / Ertel, F. / Mirus, O. / Sinning, I. / Tews, I. / Schleiff, E.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Anabena Tic22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8377
Polymers28,1401
Non-polymers6976
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anabena Tic22
hetero molecules

A: Anabena Tic22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,67414
Polymers56,2802
Non-polymers1,39412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2890 Å2
ΔGint-9 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.168, 111.190, 44.152
Angle α, β, γ (deg.)90.00, 125.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-459-

HOH

31A-499-

HOH

41A-529-

HOH

51A-543-

HOH

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Components

#1: Protein Anabena Tic22


Mass: 28140.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. (bacteria) / Strain: PCC7120 / Gene: alr0114 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Z0I2*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3948.52
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2921vapor diffusion, sitting drop9.51 M sodium citrate, 0.1 M CHES , pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K
2922vapor diffusion, sitting drop9.51 M sodium citrate, 0.15mM MgCl2 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.933
SYNCHROTRONESRF ID23-120.9798, 0.9801, 0.9760
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 14, 2009
ADSC QUANTUM 315r2CCDSep 5, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1liquid nitrogen cooled channel-cut silicon monochromatorSINGLE WAVELENGTHMx-ray1
2liquid nitrogen cooled channel-cut silicon monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.97981
30.98011
40.9761
ReflectionResolution: 1.95→36.01 Å / Num. all: 19667 / Num. obs: 19161 / % possible obs: 99.5 % / Observed criterion σ(F): -3.7 / Observed criterion σ(I): -3.7 / Redundancy: 4.1 % / Biso Wilson estimate: 31 Å2 / Rsym value: 5.6 / Net I/σ(I): 18.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 38.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→36.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.695 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): -4 / ESU R Free: 0.164 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24897 977 5.1 %RANDOM
Rwork0.19697 ---
all0.1997 19161 --
obs0.1997 18184 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.657 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å2-1.88 Å2
2--0.85 Å20 Å2
3----1.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.95→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 43 150 1960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221881
X-RAY DIFFRACTIONr_bond_other_d0.0020.021342
X-RAY DIFFRACTIONr_angle_refined_deg1.5142.0182548
X-RAY DIFFRACTIONr_angle_other_deg1.11533316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56626.14583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67215337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.774159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212030
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9891.51156
X-RAY DIFFRACTIONr_mcbond_other0.1741.5453
X-RAY DIFFRACTIONr_mcangle_it1.7921886
X-RAY DIFFRACTIONr_scbond_it2.523725
X-RAY DIFFRACTIONr_scangle_it4.214.5661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 70 -
Rwork0.317 1363 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: 15.9573 Å / Origin y: 53.3106 Å / Origin z: 1.948 Å
111213212223313233
T0.0206 Å2-0.0245 Å20.0019 Å2-0.0372 Å2-0.0112 Å2--0.0134 Å2
L0.8377 °2-0.2378 °2-0.0686 °2-1.1042 °20.3238 °2--0.6721 °2
S-0.077 Å °0.1081 Å °-0.0585 Å °-0.0223 Å °0.0632 Å °-0.0448 Å °0.0125 Å °-0.0519 Å °0.0138 Å °

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