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- PDB-2qpv: Crystal structure of uncharacterized protein Atu1531 -

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Basic information

Entry
Database: PDB / ID: 2qpv
TitleCrystal structure of uncharacterized protein Atu1531
ComponentsUncharacterized protein Atu1531
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Agrobacterium tumefaciens / Atu1531 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Hypothetical protein
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / ACETIC ACID / Polyketide cyclase / :
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsChang, C. / Binkowski, T.A. / Xu, X. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein Atu1531.
Authors: Chang, C. / Binkowski, T.A. / Xu, X. / Savchenko, A. / Joachimiak, A.
History
DepositionJul 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 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 / struct_site
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 / _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

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Assembly

Deposited unit
A: Uncharacterized protein Atu1531
B: Uncharacterized protein Atu1531
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8954
Polymers34,7752
Non-polymers1202
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
MethodPISA
2
A: Uncharacterized protein Atu1531
hetero molecules

B: Uncharacterized protein Atu1531


Theoretical massNumber of molelcules
Total (without water)34,8954
Polymers34,7752
Non-polymers1202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area2310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.852, 95.852, 76.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein Atu1531


Mass: 17387.412 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 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q8UF68, UniProt: Q7CZ16*PLUS
#2: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate, 1.5M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795224 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795224 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 17280 / Num. obs: 16220 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 48.87 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 32.688
Reflection shellResolution: 2.35→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 22.35 / % possible all: 70.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→41.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.723 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 810 5 %RANDOM
Rwork0.20878 ---
obs0.21046 15385 93.83 %-
all-15385 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.249 Å2
Baniso -1Baniso -2Baniso -3
1--1.88 Å2-0.94 Å20 Å2
2---1.88 Å20 Å2
3---2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 8 66 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9622868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14525.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.13915331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7231510
X-RAY DIFFRACTIONr_chiral_restr0.090.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2804
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21385
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8531.51380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.15922141
X-RAY DIFFRACTIONr_scbond_it1.5173832
X-RAY DIFFRACTIONr_scangle_it2.3124.5724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 50 -
Rwork0.265 884 -
obs--74.66 %
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)
12.8472-0.8952-0.11795.6136-0.64652.68510.36560.2790.1614-0.767-0.30870.2944-0.3195-0.0704-0.0569-0.02740.20490.0074-0.35110.0163-0.165844.4415.08127.8136
25.541-1.5041-7.880422.792911.888215.4536-0.62640.5022-0.2449-0.68141.12990.07990.74150.4629-0.50350.28910.307-0.41470.14-0.09460.171936.1391-1.50463.3225
37.86610.307610.808320.4515.009918.98620.1305-0.1850.4243-0.4915-0.57570.9568-0.8491-1.10640.4452-0.23660.19020.0283-0.23840.0409-0.050438.56731.643217.9478
44.5028-3.20140.62526.3118-0.81992.4503-0.3074-0.3107-0.52850.50510.34820.0640.23820.1112-0.0407-0.11140.20520.0601-0.30140.0541-0.121430.26125.741317.2621
521.4982-9.6059-7.693514.07827.172916.45730.5752-1.5189-0.35180.15890.29390.9834-0.4255-0.5271-0.8691-0.0187-0.02850.1161-0.09850.31780.135719.580521.353718.0302
658.1540.1542-9.93279.4179-1.75459.3107-0.38810.5072-0.9211-0.7521-0.07340.09370.69990.20830.46150.16460.1851-0.1085-0.32-0.0769-0.007327.27723.92735.464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1523 - 37
2X-RAY DIFFRACTION1AA39 - 10661 - 128
3X-RAY DIFFRACTION2AA16 - 3838 - 60
4X-RAY DIFFRACTION3AA107 - 133129 - 155
5X-RAY DIFFRACTION4BB1 - 1523 - 37
6X-RAY DIFFRACTION4BB39 - 10661 - 128
7X-RAY DIFFRACTION5BB16 - 3838 - 60
8X-RAY DIFFRACTION6BB107 - 133129 - 155

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