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- PDB-2r6i: Crystal structure of Atu1473 protein, a putative chaperone from A... -

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Basic information

Entry
Database: PDB / ID: 2r6i
TitleCrystal structure of Atu1473 protein, a putative chaperone from Agrobacterium tumefaciens
ComponentsUncharacterized protein Atu1473
KeywordsCHAPERONE / structural genomics / APC6123 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


proton-transporting ATP synthase complex assembly
Similarity search - Function
ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12 chaperone protein / 2-Layer Sandwich / Orthogonal Bundle ...ATP12-like fold / ATP12 ATPase / ATP12-like / ATP12-like / ATP12, ATP synthase F1-assembly protein / ATP12 orthogonal Bundle domain superfamily / ATP12, ATP synthase F1-assembly protein, N-terminal / ATP12 chaperone protein / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.59 Å
AuthorsOsipiuk, J. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Atu1473 protein, a putative chaperone from Agrobacterium tumefaciens.
Authors: Osipiuk, J. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Atu1473
B: Uncharacterized protein Atu1473


Theoretical massNumber of molelcules
Total (without water)63,8482
Polymers63,8482
Non-polymers00
Water54030
1
A: Uncharacterized protein Atu1473

A: Uncharacterized protein Atu1473


Theoretical massNumber of molelcules
Total (without water)63,8482
Polymers63,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2400 Å2
MethodPISA
2
B: Uncharacterized protein Atu1473

B: Uncharacterized protein Atu1473


Theoretical massNumber of molelcules
Total (without water)63,8482
Polymers63,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.304, 108.107, 142.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein Uncharacterized protein Atu1473 / AGR_C_2717p


Mass: 31924.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: Atu1473, AGR_C_2717 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UFC5, UniProt: A9CJ14*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 0.2M NH4(OAC), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.59→38.8 Å / Num. all: 21099 / Num. obs: 21099 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 23.8
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.51 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
PHENIXphasing
RefinementResolution: 2.59→38.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / SU B: 27.68 / SU ML: 0.273 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.751 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS program has also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.28943 1082 5.1 %RANDOM
Rwork0.2398 ---
obs0.24226 21060 99.32 %-
all-21060 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.261 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20 Å2
2--1.5 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.59→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 0 30 4232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.9735858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12324.3200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.96215726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8581534
X-RAY DIFFRACTIONr_chiral_restr0.1150.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023264
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.22020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22946
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2162
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7011.52750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16924326
X-RAY DIFFRACTIONr_scbond_it1.89231752
X-RAY DIFFRACTIONr_scangle_it2.9584.51530
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 75 -
Rwork0.332 1336 -
obs--91.27 %
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)
14.3707-0.5067-0.791612.24333.616311.10890.0041-0.11030.47430.63520.319-0.81480.03740.624-0.3231-0.05120.0339-0.0418-0.01690.04680.08412.817852.75343.8136
23.5201-1.79950.85419.6359-0.61240.95370.0382-0.143-0.0663-0.2034-0.0090.23670.2504-0.1754-0.0292-0.0324-0.0688-0.0037-0.0088-0.0076-0.0311-13.067645.109537.4205
37.5917-1.4485-0.5230.88991.53163.3777-0.1167-0.4157-0.20490.13780.09570.46370.2466-0.2120.021-0.0961-0.0451-0.0007-0.03940.09040.0842-14.477852.920153.1142
40.36190.2559-0.03920.46690.19211.29390.1306-0.1445-0.1885-0.01590.1001-0.03090.08650.0069-0.2307-0.08270.0203-0.0118-0.03280.00230.06472.235459.102750.8996
52.78011.2226-2.29764.2933-4.13667.4750.2899-0.47810.7310.25070.0152-0.1661-0.17630.4827-0.3051-0.0261-0.06770.07050.0514-0.26230.102115.839775.882859.2561
62.90181.43241.07190.85390.63410.471-0.01270.42420.4266-0.07580.25680.1395-0.14160.2133-0.244-0.0058-0.00590.04560.0935-0.00040.11034.853371.273447.581
77.7052.97314.372911.232-2.047310.19070.261-0.379-0.22440.14750.18190.6491-0.1105-0.7128-0.4429-0.00730.0234-0.0155-0.0655-0.0330.009440.321471.210843.7788
83.7081-2.42470.55099.4531.25312.3606-0.19080.00480.2012-0.0512-0.0324-0.1372-0.32780.30190.2231-0.0402-0.07350.02880.01330.039-0.083956.232978.808937.3695
92.947-1.29122.09530.8897-1.92864.642-0.0609-0.38450.22640.10830.0639-0.4968-0.21150.273-0.003-0.0915-0.06920.0135-0.02-0.08330.028557.635970.9853.1272
100.51290.05390.15870.4029-0.56091.34460.0642-0.04620.247200.15610.0508-0.0662-0.091-0.2203-0.0461-0.00460.015-0.017-0.001-0.043940.935264.69350.8288
112.74611.94262.26566.90926.61069.3618-0.0933-0.1465-0.0825-0.072-0.08650.8136-0.0892-0.76790.17980.0403-0.0811-0.04770.05550.1985-0.067827.40247.725958.9046
122.03681.2887-0.67110.8154-0.42460.2211-0.02750.2554-0.1349-0.11060.1925-0.07950.0771-0.1152-0.1650.0237-0.0206-0.03150.0730.0255-0.041238.343952.553947.3837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-6 - 715 - 28
2X-RAY DIFFRACTION2AA8 - 3629 - 57
3X-RAY DIFFRACTION3AA37 - 7858 - 99
4X-RAY DIFFRACTION4AA79 - 126100 - 147
5X-RAY DIFFRACTION5AA127 - 184148 - 205
6X-RAY DIFFRACTION6AA185 - 261206 - 282
7X-RAY DIFFRACTION7BB-6 - 715 - 28
8X-RAY DIFFRACTION8BB8 - 3629 - 57
9X-RAY DIFFRACTION9BB37 - 7858 - 99
10X-RAY DIFFRACTION10BB79 - 126100 - 147
11X-RAY DIFFRACTION11BB127 - 184148 - 205
12X-RAY DIFFRACTION12BB185 - 261206 - 282

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