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- PDB-2i6h: Structure of Protein of Unknown Function ATU0120 from Agrobacteri... -

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Basic information

Entry
Database: PDB / ID: 2i6h
TitleStructure of Protein of Unknown Function ATU0120 from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu0120
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC5905 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


TPR-like / Protein of unknown function DUF924 / Bacterial protein of unknown function (DUF924) / Tetratricopeptide repeat domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF924 domain-containing protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsOsipiuk, J. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of hypothetical protein Atu0120 from Agrobacterium tumefaciens.
Authors: Osipiuk, J. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Author states that biological unit for the protein is not yet known

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein Atu0120
B: Hypothetical protein Atu0120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2548
Polymers48,0282
Non-polymers2276
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-74 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.490, 101.193, 103.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein Atu0120 / AGR_C_189p


Mass: 24013.936 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: Atu0120 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8UJ18, UniProt: A9CKP1*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M calcium chloride, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.75→36.9 Å / Num. all: 42671 / Num. obs: 42671 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 25.1
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 7 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.95 / Num. unique all: 2971 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.971 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 2138 5 %RANDOM
Rwork0.166 ---
all0.1676 42451 --
obs0.1676 42451 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 6 454 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9264533
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7895422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41623.241216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6951539
X-RAY DIFFRACTIONr_chiral_restr0.1080.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022760
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21537
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22133
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1610.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0910.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9381.51978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35623097
X-RAY DIFFRACTIONr_scbond_it2.27431495
X-RAY DIFFRACTIONr_scangle_it3.2924.51411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 156 -
Rwork0.261 2816 -
obs-1972 95.65 %
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)
10.71520.0498-0.46032.09080.71560.5640.12050.12460.13040.0551-0.04550.0631-0.0251-0.1326-0.0750.02710.01270.00860.01180.01680.01649.942117.439610.9159
20.2476-0.1675-0.35420.20970.02460.98610.02210.02470.03760.01320.0072-0.020.0446-0.0598-0.02930.0191-0.00780.00480.01780.00510.025614.92611.878417.5652
30.46790.3322-0.00850.2433-0.08980.94440.0418-0.03330.0115-0.0212-0.0715-0.0727-0.04210.05690.02970.0031-0.00220.01190.01150.01480.036828.379321.659417.0146
423.8871-8.6125-0.514727.2338-2.401819.0970.9076-2.02311.65421.7937-1.37110.5536-2.2461-0.38850.46350.2525-0.23780.08180.2374-0.24370.036930.998929.244836.83
52.0763-0.20550.16770.1412-0.56562.50630.03480.0029-0.0127-0.04440.0276-0.0867-0.01590.0305-0.06240.01470.01540.01330.0142-0.01590.003433.177846.536213.9543
60.10650.0258-0.08940.2670.32940.54750.0053-0.0042-0.018-0.02690.01380.0175-0.04350.0028-0.01920.02930.00360.00350.0147-0.00550.022522.705153.418811.3403
71.4510.4021-0.94793.91290.79281.0160.03470.0740.03210.1066-0.03960.09930.1953-0.0460.00490.00740.0045-0.0152-0.0082-0.01430.015711.738140.27089.261
85.824.04631.63852.85620.86812.16960.4435-0.5986-0.32270.0405-0.4283-0.30240.0228-0.4196-0.0152-0.0083-0.0575-0.0050.1126-0.02620.00725.668242.75827.7537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2823 - 50
2X-RAY DIFFRACTION2AA29 - 9051 - 112
3X-RAY DIFFRACTION3AA91 - 170113 - 192
4X-RAY DIFFRACTION4AA171 - 179193 - 201
5X-RAY DIFFRACTION5BB4 - 3526 - 57
6X-RAY DIFFRACTION6BB36 - 12258 - 144
7X-RAY DIFFRACTION7BB123 - 147145 - 169
8X-RAY DIFFRACTION8BB148 - 179170 - 201

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