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- PDB-4rd7: The crystal structure of a Cupin 2 conserved barrel domain protei... -

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Basic information

Entry
Database: PDB / ID: 4rd7
TitleThe crystal structure of a Cupin 2 conserved barrel domain protein from Salinispora arenicola CNS-205
ComponentsCupin 2 conserved barrel domain protein
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / Enzyme Discovery for Natural Product Biosynthesis / NatPro
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupin 2 conserved barrel domain protein
Similarity search - Component
Biological speciesSalinispora arenicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.571 Å
AuthorsTan, K. / Gu, M. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: To be Published
Title: The crystal structure of a Cupin 2 conserved barrel domain protein from Salinispora arenicola CNS-205
Authors: Tan, K. / Gu, M. / Clancy, S. / Phillips Jr., G.N. / Joachimiak, A.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1447
Polymers14,5711
Non-polymers5726
Water1,76598
1
A: Cupin 2 conserved barrel domain protein
hetero molecules

A: Cupin 2 conserved barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,28814
Polymers29,1432
Non-polymers1,14512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5500 Å2
ΔGint-122 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.687, 43.687, 132.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cupin 2 conserved barrel domain protein


Mass: 14571.407 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora arenicola (bacteria) / Strain: CNS-205 / Gene: Sare_2150 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pGrow7-K / References: UniProt: A8M0K5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.6M Ammonium Sulfate, 0.1M MES:NaOH, 10% (v/v) Dioxane, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.57→36.5 Å / Num. all: 18841 / Num. obs: 18841 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 14 % / Biso Wilson estimate: 13.76 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 47.2
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.9 / Num. unique all: 891 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDBuilder/HKL3000phasing
MLPHAREBuilder/HKL3000phasing
DMBuilder/HKL3000model building
DENZOBuilder/HKL3000data reduction
SCALEPACKBuilder/HKL3000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMBuilder/HKL3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.571→36.497 Å / SU ML: 0.12 / σ(F): 1.36 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 909 4.85 %random
Rwork0.1555 ---
obs0.1574 18758 99.84 %-
all-18758 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.571→36.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 31 98 1053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006982
X-RAY DIFFRACTIONf_angle_d1.1051346
X-RAY DIFFRACTIONf_dihedral_angle_d13.744339
X-RAY DIFFRACTIONf_chiral_restr0.079137
X-RAY DIFFRACTIONf_plane_restr0.005174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5713-1.66980.20411480.13352875X-RAY DIFFRACTION99
1.6698-1.79870.20971440.1292888X-RAY DIFFRACTION100
1.7987-1.97970.18711500.12132953X-RAY DIFFRACTION100
1.9797-2.26610.19051610.12782934X-RAY DIFFRACTION100
2.2661-2.85490.20081360.16613009X-RAY DIFFRACTION100
2.8549-36.50690.191700.17573190X-RAY DIFFRACTION100

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