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- PDB-3dnh: The crystal structure of the protein Atu2129 (unknown function) f... -

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Basic information

Entry
Database: PDB / ID: 3dnh
TitleThe crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58
Componentsuncharacterized protein Atu2129
Keywordsstructural genomics / unknown function / APC6114 / protein Atu2129 / Agrobacterium tumefaciens str. C58 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase / PNP-oxidase-like / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Alpha-Beta Barrel ...Pyridoxamine 5'-phosphate oxidase / PNP-oxidase-like / Haem oxygenase HugZ-like superfamily / Split barrel-like / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Pyridoxamine 5-phosphate oxidase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsTan, K. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein Atu2129 (unknown function) from Agrobacterium tumefaciens str. C58
Authors: Tan, K. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein Atu2129
B: uncharacterized protein Atu2129


Theoretical massNumber of molelcules
Total (without water)55,4602
Polymers55,4602
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-24 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.651, 66.830, 69.967
Angle α, β, γ (deg.)90.00, 108.19, 90.00
Int Tables number4
Space group name H-MP1211
Detailsauthors state that the biological unit is experimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein uncharacterized protein Atu2129


Mass: 27730.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Strain: str. C58 / Gene: AGR_C_3862, Atu2129 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9CI98
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris, 0.2M Na(OAc), 30% PEG 8K, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929, 0.97942
DetectorType: SBC-3 / Detector: CCD / Date: Jan 30, 2008 / Details: mirror
RadiationMonochromator: Si crystal 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979421
ReflectionResolution: 1.94→30 Å / Num. all: 34554 / Num. obs: 34554 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.8
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.67 / Num. unique all: 2833 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→29.76 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.276 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.174 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23804 1726 5 %RANDOM
Rwork0.1867 ---
all0.18928 32787 --
obs0.18928 32787 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.966 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.94→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 0 289 3830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9884930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5065465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64322.069145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30415582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2151540
X-RAY DIFFRACTIONr_chiral_restr0.1230.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022721
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.821.52396
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31623746
X-RAY DIFFRACTIONr_scbond_it2.21631367
X-RAY DIFFRACTIONr_scangle_it3.3044.51182
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.943→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 111 -
Rwork0.257 2256 -
obs-2367 93.01 %
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)
128.489614.3047-7.53648.70330.079111.8059-0.04250.74281.5365-0.5207-0.4564-0.2678-0.71770.34280.49890.037-0.1448-0.0589-0.140.14580.21624.25464.1687.578
23.76540.14811.74432.16860.77822.9861-0.1097-0.17660.2561-0.1215-0.0302-0.0004-0.0599-0.06650.1399-0.12720.02590.0009-0.249-0.0174-0.191211.12949.2511.108
34.1242.78351.298.11120.51633.1417-0.20240.3231-0.2432-0.46980.2178-0.0729-0.16090.0187-0.0154-0.0507-0.00790.0545-0.2345-0.0303-0.28822.95339.151-7.982
437.8558-18.6598-9.125116.63282.84217.2642-0.4951-2.69241.69290.77821.0158-0.1672-0.1435-0.594-0.5206-0.02820.11450.04720.2457-0.1983-0.070518.31254.69332.847
53.0058-0.86030.35752.01740.10761.8676-0.1244-0.29380.1763-0.00190.107300.11650.27530.0171-0.11630.01590.0202-0.1007-0.0441-0.241529.79244.7620.216
64.3898-0.7591-0.33515.70591.42215.2807-0.2154-0.3822-0.50430.16780.30980.05420.63750.3428-0.09440.11420.13540.0394-0.05890.0455-0.235936.58324.24426.284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 126 - 14
2X-RAY DIFFRACTION2AA24 - 17326 - 175
3X-RAY DIFFRACTION3AA174 - 254176 - 256
4X-RAY DIFFRACTION4BB5 - 127 - 14
5X-RAY DIFFRACTION5BB21 - 17323 - 175
6X-RAY DIFFRACTION6BB174 - 252176 - 254

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