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

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Basic information

Entry
Database: PDB / ID: 7dyc
TitleCrystal structure of the chemically synthesized mk2h_deltaMILPYS peptide homodimer in complex with malate
Componentsmk2h_deltaMILPYS protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homology(2S)-2-hydroxybutanedioic acid / D-MALATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 21, 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)20,7656
Polymers20,4964
Non-polymers2682
Water1,71195
1
A: mk2h_deltaMILPYS protein
hetero molecules

A: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5164
Polymers10,2482
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4670 Å2
ΔGint-19 kcal/mol
Surface area4990 Å2
MethodPISA
2
B: mk2h_deltaMILPYS protein
D: mk2h_deltaMILPYS protein


Theoretical massNumber of molelcules
Total (without water)10,2482
Polymers10,2482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-12 kcal/mol
Surface area4910 Å2
MethodPISA
3
C: mk2h_deltaMILPYS protein
hetero molecules

C: mk2h_deltaMILPYS protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5164
Polymers10,2482
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4610 Å2
ΔGint-13 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.278, 52.278, 146.731
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: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2100 mM DL Malic acid pH 7.0

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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: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10931 / % possible obs: 99.7 % / Redundancy: 21.19 % / CC1/2: 0.998 / Net I/σ(I): 17.17
Reflection shellResolution: 2.3→2.44 Å / Num. unique obs: 1638 / CC1/2: 0.857

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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: 7DXZ

7dxz


Resolution: 2.3→33.225 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1092 10 %
Rwork0.2255 9831 -
obs0.2291 10923 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.19 Å2 / Biso mean: 38.7176 Å2 / Biso min: 17.25 Å2
Refinement stepCycle: final / Resolution: 2.3→33.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 18 95 1389
Biso mean--45.96 46.22 -
Num. residues----168
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3003-2.40490.30841360.26761200
2.4049-2.53170.27391310.25341186
2.5317-2.69020.28521360.24881212
2.6902-2.89780.32441340.24441216
2.8978-3.18930.25691320.23451204
3.1893-3.65030.2431380.20311226
3.6503-4.5970.21061400.18561262
4.597-33.2250.28711450.24331325

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