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- PDB-4p0e: YhdE E33A (p212121 space group) -

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Basic information

Entry
Database: PDB / ID: 4p0e
TitleYhdE E33A (p212121 space group)
ComponentsMaf-like protein YhdE
KeywordsUNKNOWN FUNCTION / YhdE E33A p212121
Function / homology
Function and homology information


dTTP diphosphatase activity / UTP diphosphatase activity / NADH pyrophosphatase activity / nucleotide diphosphatase / nucleoside triphosphate diphosphatase activity / nucleotide metabolic process / manganese ion binding / identical protein binding / 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
PHOSPHATE ION / dTTP/UTP pyrophosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsJia, Z. / Zheng, J. / Jin, J. / Wang, N.
CitationJournal: To Be Published
Title: YhdE E33A
Authors: Jia, Z. / Zheng, J. / Jin, J. / Wang, N.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Structure summary
Revision 1.2Jul 9, 2014Group: Structure summary
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maf-like protein YhdE
B: Maf-like protein YhdE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,88511
Polymers41,0222
Non-polymers8629
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-111 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.883, 85.897, 88.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 3 - 189 / Label seq-ID: 2 - 188

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Maf-like protein YhdE


Mass: 20511.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhdE, b3248, JW3217 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P25536
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Magnesium Sulfate, 0.1M MES buffer, 10-15% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 16082 / % possible obs: 99.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.063 / Χ2: 1.166 / Net I/av σ(I): 29.204 / Net I/σ(I): 13.3 / Num. measured all: 98279
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.384.40.29915071.17194.2
2.38-2.485.10.27515271.14597.1
2.48-2.595.70.24215891.16499.7
2.59-2.736.20.19315951.16100
2.73-2.96.50.15516081.111100
2.9-3.126.70.1116031.106100
3.12-3.436.70.06916161.103100
3.43-3.936.70.04816251.123100
3.93-4.956.70.03516591.165100
4.95-306.30.03517531.40399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.547 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 804 5 %RANDOM
Rwork0.1886 15235 --
obs0.1912 16039 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.1 Å2 / Biso mean: 38.103 Å2 / Biso min: 20.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.3→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 45 118 3035
Biso mean--71.78 38.58 -
Num. residues----377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192946
X-RAY DIFFRACTIONr_bond_other_d0.0050.022854
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.9874001
X-RAY DIFFRACTIONr_angle_other_deg1.15336530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43824.242132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4215496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4121524
X-RAY DIFFRACTIONr_chiral_restr0.0880.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023345
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02647
Refine LS restraints NCS

Ens-ID: 1 / Number: 10496 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 57 -
Rwork0.228 1028 -
all-1085 -
obs--93.37 %

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