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- PDB-4p0u: YhdE E33A p4 space group -

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Basic information

Entry
Database: PDB / ID: 4p0u
TitleYhdE E33A p4 space group
ComponentsMaf-like protein YceF
KeywordsUNKNOWN FUNCTION / YhdE / E33A mutant
Function / homologyMaf protein - #10 / Maf protein / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsZheng, J. / Jin, J. / Wang, N. / Jia, Z.
CitationJournal: To Be Published
Title: YhdE E33A p4 space group
Authors: Zheng, J. / Jin, J. / Wang, N. / Jia, Z.
History
DepositionFeb 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 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_assembly_gen / pdbx_struct_assembly_prop / 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_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 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

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Assembly

Deposited unit
A: Maf-like protein YceF
B: Maf-like protein YceF


Theoretical massNumber of molelcules
Total (without water)41,3932
Polymers41,3932
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.066, 71.066, 78.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 187 / Label seq-ID: 1 - 185

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

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Components

#1: Protein Maf-like protein YceF


Mass: 20696.518 Da / Num. of mol.: 2 / Fragment: UNP residues 3-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KTE171 / Gene: yceF, A31Q_03875 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L3WSY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Magnesium Sulfate 0.1M MES buffer 10%~15% PEG8000

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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: 2.35→25 Å / Num. obs: 16184 / % possible obs: 98.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.051 / Χ2: 1.27 / Net I/av σ(I): 29.533 / Net I/σ(I): 17.3 / Num. measured all: 65762
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.433.10.19213791.6484
2.43-2.533.90.19516381.24499.9
2.53-2.654.10.14616431.278100
2.65-2.794.10.12416121.245100
2.79-2.964.20.09716561.224100
2.96-3.194.20.0716251.26100
3.19-3.514.20.05116231.219100
3.51-4.014.20.04216581.509100
4.01-5.054.30.0316661.22499.9
5.05-254.20.02616841.02299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.24 Å24.75 Å
Translation6.24 Å24.75 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→24.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 7.278 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.418 / 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
Rfree0.2375 817 5.1 %RANDOM
Rwork0.1834 15344 --
obs0.186 16161 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.33 Å2 / Biso mean: 30.04 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.36→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 0 134 3000
Biso mean---29.35 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192904
X-RAY DIFFRACTIONr_bond_other_d0.0050.022859
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9743937
X-RAY DIFFRACTIONr_angle_other_deg1.13336542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02524.198131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2515498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3071524
X-RAY DIFFRACTIONr_chiral_restr0.090.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023334
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02646
Refine LS restraints NCS

Ens-ID: 1 / Number: 10752 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.36→2.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 59 -
Rwork0.234 1000 -
all-1059 -
obs--89.82 %

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