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- PDB-3d01: Crystal structure of the protein Atu1372 with unknown function fr... -

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Basic information

Entry
Database: PDB / ID: 3d01
TitleCrystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein with unknown function / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyYjgF/chorismate_mutase-like, putative endoribonuclease / Endoribonuclease L-PSP/chorismate mutase-like / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Endoribonuclease L-PSP/chorismate mutase-like domain-containing protein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens.
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,90924
Polymers208,77012
Non-polymers2,13912
Water19,3481074
1
A: Uncharacterized protein
I: Uncharacterized protein
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7276
Polymers52,1923
Non-polymers5353
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-36.6 kcal/mol
Surface area18250 Å2
MethodPISA
2
E: Uncharacterized protein
G: Uncharacterized protein
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7276
Polymers52,1923
Non-polymers5353
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-34.4 kcal/mol
Surface area18200 Å2
MethodPISA
3
C: Uncharacterized protein
F: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9057
Polymers52,1923
Non-polymers7134
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-33.6 kcal/mol
Surface area18190 Å2
MethodPISA
4
B: Uncharacterized protein
D: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5495
Polymers52,1923
Non-polymers3562
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-32.5 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.623, 93.600, 93.628
Angle α, β, γ (deg.)68.20, 67.87, 68.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Uncharacterized protein


Mass: 17397.490 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Strain: C58 / Gene: GI:17935272, AGR_C_2535, Atu1372 / Plasmid: pDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A9CJ63
#2: Chemical
ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H18O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1074 / 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

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-tris pH 5.5, 0.2M NH4(OAC), 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794, 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2006 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97961
ReflectionResolution: 1.7→83.62 Å / Num. all: 274501 / Num. obs: 266266 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.33
Reflection shellResolution: 1.7→1.745 Å / Redundancy: 4 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 1.5 / Num. unique all: 21313 / % possible all: 92.08

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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: MAD / Resolution: 1.7→46.13 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.893 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21411 14230 5.1 %RANDOM
Rwork0.17888 ---
all0.18066 266266 --
obs0.18066 266266 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.647 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.15 Å2-0.21 Å2
2--0.16 Å2-0.24 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14016 0 144 1074 15234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214328
X-RAY DIFFRACTIONr_bond_other_d0.0010.029420
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9819375
X-RAY DIFFRACTIONr_angle_other_deg0.925323150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.66651864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58124.746571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.48152350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5491584
X-RAY DIFFRACTIONr_chiral_restr0.0860.22336
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022680
X-RAY DIFFRACTIONr_nbd_refined0.2150.23154
X-RAY DIFFRACTIONr_nbd_other0.1950.210472
X-RAY DIFFRACTIONr_nbtor_refined0.1690.27131
X-RAY DIFFRACTIONr_nbtor_other0.0860.27319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2835
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.212
X-RAY DIFFRACTIONr_mcbond_it1.6331.511256
X-RAY DIFFRACTIONr_mcbond_other0.8381.53861
X-RAY DIFFRACTIONr_mcangle_it2.027214923
X-RAY DIFFRACTIONr_scbond_it4.10435333
X-RAY DIFFRACTIONr_scangle_it5.4464.54452
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 1033 -
Rwork0.256 18592 -
obs-19625 92.08 %

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