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- PDB-2hwj: Crystal structure of protein Atu1540 from Agrobacterium tumefaciens -

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Basic information

Entry
Database: PDB / ID: 2hwj
TitleCrystal structure of protein Atu1540 from Agrobacterium tumefaciens
ComponentsHypothetical protein Atu1540
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / Hypothetical protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Putative ParB-like nuclease / Uncharacterised conserved protein UCP029669 / Putative ParB-like nuclease / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin superfamily / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Alpha-Beta Complex / Orthogonal Bundle ...Putative ParB-like nuclease / Uncharacterised conserved protein UCP029669 / Putative ParB-like nuclease / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/Sulfiredoxin superfamily / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chromosome partitioning protein ParB / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsChang, C. / Xu, X. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein Atu1540 from Agrobacterium tumefaciens
Authors: Chang, C. / Xu, X. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionAug 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 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 / 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: Hypothetical protein Atu1540
B: Hypothetical protein Atu1540
C: Hypothetical protein Atu1540
D: Hypothetical protein Atu1540
E: Hypothetical protein Atu1540
F: Hypothetical protein Atu1540


Theoretical massNumber of molelcules
Total (without water)142,6056
Polymers142,6056
Non-polymers00
Water1,71195
1
A: Hypothetical protein Atu1540
B: Hypothetical protein Atu1540
C: Hypothetical protein Atu1540
D: Hypothetical protein Atu1540


Theoretical massNumber of molelcules
Total (without water)95,0704
Polymers95,0704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-22 kcal/mol
Surface area35460 Å2
MethodPISA
2
E: Hypothetical protein Atu1540
F: Hypothetical protein Atu1540

E: Hypothetical protein Atu1540
F: Hypothetical protein Atu1540


Theoretical massNumber of molelcules
Total (without water)95,0704
Polymers95,0704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
3
E: Hypothetical protein Atu1540
F: Hypothetical protein Atu1540

E: Hypothetical protein Atu1540
F: Hypothetical protein Atu1540

A: Hypothetical protein Atu1540
B: Hypothetical protein Atu1540
C: Hypothetical protein Atu1540
D: Hypothetical protein Atu1540

A: Hypothetical protein Atu1540
B: Hypothetical protein Atu1540
C: Hypothetical protein Atu1540
D: Hypothetical protein Atu1540


Theoretical massNumber of molelcules
Total (without water)285,21012
Polymers285,21012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
crystal symmetry operation2_565-x,-y+1,z+1/21
crystal symmetry operation4_565x,-y+1,-z1
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29040 Å2
ΔGint-51 kcal/mol
Surface area103850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.079, 173.749, 142.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Hypothetical protein Atu1540 / AGR_C_2837p


Mass: 23767.508 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / ATCC 33970 / Plasmid: pET derivatives / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 derivatives / References: UniProt: Q8UF59, UniProt: A9CIY5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl, 0.01M Magnesium chloride, 22% PEG400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 49927 / Num. obs: 49478 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 34
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4504 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.912 / SU B: 26.699 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.54 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27261 2486 5.1 %RANDOM
Rwork0.1981 ---
all0.20183 46524 --
obs0.20183 46524 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å20 Å2
2---3.16 Å20 Å2
3---4.03 Å2
Refinement stepCycle: LAST / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 0 0 95 9355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0219511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3291.9512833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.14351147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50822.259478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.706151652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8115108
X-RAY DIFFRACTIONr_chiral_restr0.1630.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027296
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.24546
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.26437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2641.55860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97729170
X-RAY DIFFRACTIONr_scbond_it3.47434112
X-RAY DIFFRACTIONr_scangle_it5.2184.53659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 167 -
Rwork0.347 2960 -
obs--85.58 %
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)
12.28570.3013-0.30075.0043-1.47594.75690.10790.01460.2242-0.2912-0.0702-0.00230.1924-0.0931-0.0377-0.20290.1065-0.0453-0.12410.0519-0.07855.226339.1602-5.0935
25.7666-0.70091.54565.5618-1.60174.4041-0.0990.04050.21690.27710.0879-0.4528-0.41920.04350.0111-0.12650.06960.0031-0.1762-0.00530.152618.063957.42862.8564
32.83181.3940.53396.9901-1.87063.3574-0.0655-0.3750.53820.7972-0.105-0.3852-0.6225-0.14040.17060.06510.1082-0.0567-0.1419-0.2178-0.331215.009342.678628.8357
45.9415-1.1472-2.10974.31730.56926.3374-0.0218-0.15020.21850.19320.264-0.02520.1566-0.2541-0.2421-0.19110.03590.0095-0.0609-0.0507-0.40036.67522.796120.3087
51.34060.31140.47761.6077-0.71860.99560.08990.08610.1621-0.2212-0.1106-0.21730.12320.02740.0207-0.00220.08030.11-0.07910.0022-0.02828.551322.6547-9.0107
61.9217-0.2703-0.54512.29540.46281.44990.049-0.01180.13510.098-0.0395-0.25650.1214-0.1227-0.0095-0.04060.025-0.0273-0.0296-0.0336-0.061326.875512.420312.1144
73.90121.2149-1.0774.499-2.1896.19840.0945-0.26950.56030.7032-0.2657-0.8925-0.20180.50.1712-0.27880.0087-0.304-0.1524-0.04680.387342.791436.704220.4203
89.2469-1.78961.2025.952-1.55036.2156-0.12670.09520.50340.104-0.2994-0.7858-0.57570.37520.4262-0.2721-0.04260.0399-0.16590.11670.461640.463648.81940.5576
95.6162-0.52330.88417.43760.0144.2099-0.07840.00260.27070.2538-0.0619-0.4139-0.61880.38210.14030.0573-0.0875-0.075-0.1744-0.0273-0.09638.819386.051-14.484
105.8451-0.6466-0.01433.4443-1.96949.5799-0.058-0.0305-0.12970.17650.22360.17480.13580.0331-0.1657-0.16150.03540.0165-0.2390.0318-0.0297-2.751668.0645-23.6413
115.0529-0.37893.27029.2624-0.39936.4707-0.241-0.22510.2157-0.06720.32550.9094-0.8836-0.9322-0.0844-0.25270.17750.1753-0.00950.21240.1284-22.13990.1458-29.7127
1212.8058-1.2369-3.2658.3155-0.791311.3423-0.2204-0.12040.5738-0.35890.30251.1547-1.62-0.5206-0.08210.56090.11450.0245-0.30030.05220.2194-7.9626108.1675-25.6799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1334 - 133
2X-RAY DIFFRACTION2AA134 - 204134 - 204
3X-RAY DIFFRACTION3BB7 - 1337 - 133
4X-RAY DIFFRACTION4BB134 - 204134 - 204
5X-RAY DIFFRACTION5CC5 - 1335 - 133
6X-RAY DIFFRACTION6CC134 - 204134 - 204
7X-RAY DIFFRACTION7DD6 - 1336 - 133
8X-RAY DIFFRACTION8DD134 - 204134 - 204
9X-RAY DIFFRACTION9EE7 - 1337 - 133
10X-RAY DIFFRACTION10EE134 - 204134 - 204
11X-RAY DIFFRACTION11FF6 - 1336 - 133
12X-RAY DIFFRACTION12FF134 - 204134 - 204

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