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- PDB-4heb: The Crystal structure of Maf protein of Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 4heb
TitleThe Crystal structure of Maf protein of Bacillus subtilis
ComponentsSeptum formation protein Maf
KeywordsCELL CYCLE / Bacillus subtilis / Maf proteins / nucleoside triphosphate pyrophosphatase / Structural Genomics / Structural Genomics Consortium / SGC
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
dTTP/UTP pyrophosphatase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsDong, A. / Dombrovski, L. / Brown, G. / Flick, R. / Tchigvintsev, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Iakounine, A. / Min, J. ...Dong, A. / Dombrovski, L. / Brown, G. / Flick, R. / Tchigvintsev, D. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Iakounine, A. / Min, J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Chem.Biol. / Year: 2013
Title: Biochemical and structural studies of conserved maf proteins revealed nucleotide pyrophosphatases with a preference for modified nucleotides.
Authors: Tchigvintsev, A. / Tchigvintsev, D. / Flick, R. / Popovic, A. / Dong, A. / Xu, X. / Brown, G. / Lu, W. / Wu, H. / Cui, H. / Dombrowski, L. / Joo, J.C. / Beloglazova, N. / Min, J. / ...Authors: Tchigvintsev, A. / Tchigvintsev, D. / Flick, R. / Popovic, A. / Dong, A. / Xu, X. / Brown, G. / Lu, W. / Wu, H. / Cui, H. / Dombrowski, L. / Joo, J.C. / Beloglazova, N. / Min, J. / Savchenko, A. / Caudy, A.A. / Rabinowitz, J.D. / Murzin, A.G. / Yakunin, A.F.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septum formation protein Maf
B: Septum formation protein Maf


Theoretical massNumber of molelcules
Total (without water)47,51033
Polymers47,5102
Non-polymers031
Water1,42379
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.550, 85.950, 95.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Septum formation protein Maf


Mass: 23754.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: maf, BSU28050 / Plasmid: p15-TVL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02169
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 31 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 3500, 0.1 M succinate acid pH7.0, vapor diffusion hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 24272 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 43 Å2 / Rsym value: 0.107 / Net I/σ(I): 19.7
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 0.884 % / Num. unique all: 1172 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data scaling
MOLREP10.2..35phasing
BUSTER2.10.0refinement
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX2

1ex2


Resolution: 2.26→25.74 Å / Cor.coef. Fo:Fc: 0.9187 / Cor.coef. Fo:Fc free: 0.8867 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 638 2.64 %RANDOM
Rwork0.2146 ---
obs0.2155 24200 99.85 %-
Displacement parametersBiso max: 134.6 Å2 / Biso mean: 50.6288 Å2 / Biso min: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1--13.8173 Å20 Å20 Å2
2--12.8853 Å20 Å2
3---0.9319 Å2
Refine analyzeLuzzati coordinate error obs: 0.329 Å
Refinement stepCycle: LAST / Resolution: 2.26→25.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 31 79 2841
LS refinement shellResolution: 2.26→2.36 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2627 61 2.13 %
Rwork0.2153 2808 -
all0.2162 2869 -
obs--99.85 %
Refinement TLS params.

S22: -0.0467 Å ° / 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 °)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)
10.9202-0.2447-0.85951.50680.41992.9191-0.0784-0.2383-0.175-0.0926-0.05330.09070.35660.1251-0.031-0.0071-0.0256-0.09660.0483-0.107726.0884-8.5391-6.872
21.41150.2164-1.52781.6915-0.40483.9160.04970.2713-0.09760.11370.2231-0.0841-0.4829-0.003-0.04510.039-0.0355-0.1288-0.021-0.12142.938-4.39966.9385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 185
2X-RAY DIFFRACTION2{ B|* }B2 - 188

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