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- PDB-7dvc: Crystal structure of the computationally designed reDPBB_sym1 protein -

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Basic information

Entry
Database: PDB / ID: 7dvc
TitleCrystal structure of the computationally designed reDPBB_sym1 protein
ComponentsreDPBB_sym1 protein
KeywordsCHAPERONE / Double psi beta barrel
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.705 Å
AuthorsYagi, S. / Tagami, S. / Padhi, A.K. / Zhang, K.Y.J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H01328 Japan
CitationJournal: 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.
History
DepositionJan 13, 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
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: reDPBB_sym1 protein
C: reDPBB_sym1 protein
E: reDPBB_sym1 protein
F: reDPBB_sym1 protein
B: reDPBB_sym1 protein
D: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,73820
Polymers56,1246
Non-polymers61414
Water12,899716
1
A: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4604
Polymers9,3541
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area4740 Å2
MethodPISA
2
C: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5195
Polymers9,3541
Non-polymers1654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
3
E: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4483
Polymers9,3541
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4650 Å2
MethodPISA
4
F: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4132
Polymers9,3541
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
5
B: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4483
Polymers9,3541
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4680 Å2
MethodPISA
6
D: reDPBB_sym1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4483
Polymers9,3541
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.151, 98.151, 177.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
reDPBB_sym1 protein


Mass: 9353.974 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 3.8 Å3/Da / Density % sol: 67.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium acetate pH3.8, 2M NaCl, 400 mM Lithium sulfate

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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 MX225-HS / Detector: CCD / Date: Apr 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 94555 / % possible obs: 99.6 % / Redundancy: 28 % / CC1/2: 1 / Net I/σ(I): 33
Reflection shellResolution: 1.7→1.81 Å / Num. unique obs: 14747 / CC1/2: 0.96

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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: Computationally Designed Mode

Resolution: 1.705→47.298 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.49 / Phase error: 16.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 1999 2.11 %
Rwork0.1656 92531 -
obs0.1658 94530 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.86 Å2 / Biso mean: 30.9935 Å2 / Biso min: 12.56 Å2
Refinement stepCycle: final / Resolution: 1.705→47.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 29 716 4653
Biso mean--34.28 44.1 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.705-1.74720.26951330.2596617395
1.7472-1.79440.22631410.22486540100
1.7944-1.84720.21241430.20186571100
1.8472-1.90680.19241400.18936516100
1.9068-1.9750.18421430.17446569100
1.975-2.0540.18151410.17766570100
2.054-2.14750.19621430.16896564100
2.1475-2.26080.18441420.16826606100
2.2608-2.40240.18081430.16736618100
2.4024-2.58790.1661430.16766637100
2.5879-2.84830.16971440.16226642100
2.8483-3.26030.16551450.15796695100
3.2603-4.10730.15611460.13536779100
4.1073-47.2980.17771520.16737051100

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