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- PDB-1exc: CRYSTAL STRUCTURE OF B. SUBTILIS MAF PROTEIN COMPLEXED WITH D-(UTP) -

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Basic information

Entry
Database: PDB / ID: 1exc
TitleCRYSTAL STRUCTURE OF B. SUBTILIS MAF PROTEIN COMPLEXED WITH D-(UTP)
ComponentsPROTEIN MAF
KeywordsSTRUCTURAL GENOMICS / B.subtilis Maf protein complexed with dUTP / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


dTTP diphosphatase activity / UTP diphosphatase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / cytoplasm
Similarity search - Function
Nucleoside triphosphate pyrophosphatase Maf-like protein / Maf-like protein / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DEOXYURIDINE-5'-TRIPHOSPHATE / dTTP/UTP pyrophosphatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsMinasov, G. / Teplova, M. / Stewart, G.C. / Koonin, E.V. / Anderson, W.F. / Egli, M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.
Authors: Minasov, G. / Teplova, M. / Stewart, G.C. / Koonin, E.V. / Anderson, W.F. / Egli, M.
History
DepositionMay 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: PROTEIN MAF
B: PROTEIN MAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5427
Polymers42,6472
Non-polymers1,8965
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-5 kcal/mol
Surface area18450 Å2
MethodPISA
2
A: PROTEIN MAF
hetero molecules

B: PROTEIN MAF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5427
Polymers42,6472
Non-polymers1,8965
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area4240 Å2
ΔGint-6 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.10, 86.58, 93.73
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chains A and B.

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Components

#1: Protein PROTEIN MAF


Mass: 21323.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02169
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H15N2O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
38 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 12658 / Num. obs: 12658 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 15.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.287 / Num. unique all: 1261 / % possible all: 92
Reflection shell
*PLUS
% possible obs: 92 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.7→17 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1211 -RANDOM 10% of the observed data
Rwork0.197 ---
all-12260 --
obs-12260 85.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 113 140 3179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_torsion_deg25
X-RAY DIFFRACTIONc_torsion_impr_deg0.92

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