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- PDB-7dxz: Crystal structure of the chemically synthesized mk2h_deltaMILPYS ... -

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Basic information

Entry
Database: PDB / ID: 7dxz
TitleCrystal structure of the chemically synthesized mk2h_deltaMILPYS peptide homodimer in complex with malonate
Componentsmk2h_deltaMILPYS protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homologyMALONIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYagi, S. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
Citation
Journal: J.Am.Chem.Soc. / Year: 2021
Title: Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
#1: Journal: Biorxiv / Year: 2021
Title: Seven amino acid types suffice to reconstruct the core fold of RNA polymerase.
Authors: Yagi, S. / Padhi, A.K. / Vucinic, J. / Barbe, S. / Schiex, T. / Nakagawa, R. / Simoncini, D. / Zhang, K.Y.J. / Tagami, S.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mk2h_deltaMILPYS protein
B: mk2h_deltaMILPYS protein
C: mk2h_deltaMILPYS protein
D: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,22511
Polymers20,4964
Non-polymers7287
Water2,198122
1
A: mk2h_deltaMILPYS protein
hetero molecules

A: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6646
Polymers10,2482
Non-polymers4164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4770 Å2
ΔGint-24 kcal/mol
Surface area4860 Å2
MethodPISA
2
B: mk2h_deltaMILPYS protein
C: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5605
Polymers10,2482
Non-polymers3123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-23 kcal/mol
Surface area4780 Å2
MethodPISA
3
D: mk2h_deltaMILPYS protein
hetero molecules

D: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6646
Polymers10,2482
Non-polymers4164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area5200 Å2
ΔGint-41 kcal/mol
Surface area5080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 52.070, 146.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide
mk2h_deltaMILPYS protein


Mass: 5124.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3000 M Sodium malonate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 18940 / % possible obs: 99.8 % / Redundancy: 21.37 % / CC1/2: 1 / Net I/σ(I): 31.49
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 2985 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DXX

7dxx


Resolution: 1.9→28.415 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 1896 10.03 %
Rwork0.1948 17013 -
obs0.1995 18909 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122 Å2 / Biso mean: 37.656 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 1.9→28.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 49 122 1456
Biso mean--54.92 44.22 -
Num. residues----169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.94750.30421370.29141190
1.9475-2.00020.26151340.21031218
2.0002-2.0590.23581310.19821170
2.059-2.12550.24371300.20311176
2.1255-2.20140.22461300.20031204
2.2014-2.28950.25741350.21281207
2.2895-2.39370.27131340.20741190
2.3937-2.51980.25351350.21241197
2.5198-2.67750.25711320.2031211
2.6775-2.88410.23571370.21171209
2.8841-3.1740.26481350.19691219
3.174-3.63250.22511390.16891234
3.6325-4.57340.20171390.15111259
4.5734-28.4150.25931480.21321329

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