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- PDB-2pfw: CRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELL... -

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Basic information

Entry
Database: PDB / ID: 2pfw
TitleCRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.90 A RESOLUTION
ComponentsCupin 2, conserved barrel domain protein
KeywordsUNKNOWN FUNCTION / CUPIN DOMAIN / CUPIN 2 CONSERVED BARREL DOMAIN PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Pectin degradation protein KdgF / 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 speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Cupin 2 conserved barrel domain protein (YP_751781.1) from Shewanella frigidimarina NCIMB 400 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,0767
Polymers25,7662
Non-polymers3105
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-4 kcal/mol
Surface area9940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 73.140, 73.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Cupin 2, conserved barrel domain protein


Mass: 12882.890 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Strain: NCIMB 400 / Gene: YP_751781.1, Sfri_3105 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q07YH2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.04 Å3/Da / Density % sol: 59.47 %
Description: THE STRUCTURE WAS SOLVED IN SPACE GROUP P41212. MAD PHASING STATISTICS AND AUTOMATED MODEL BUILDING LOOKED REASONABLE. AFTER INITIAL REFINEMENT IN P41212, THE R AND FREE-R FACTORS WERE ...Description: THE STRUCTURE WAS SOLVED IN SPACE GROUP P41212. MAD PHASING STATISTICS AND AUTOMATED MODEL BUILDING LOOKED REASONABLE. AFTER INITIAL REFINEMENT IN P41212, THE R AND FREE-R FACTORS WERE HIGHER THAN EXPECTED. THE STRUCTURE WAS THEN EXPANDED TO SPACEGROUPS P41 AND P212121. TWINNING TESTS IN BOTH SPACE GROUPS YIELDED IMPROVED STATISTICS. HOWEVER, ONLY THE P212121 TWIN REFINEMENT GAVE THE EXPECTED R/FREE-R VALUES. SUBSEQUENTLY, THE MAD PHASING WAS REPEATED IN SPACE GROUP P212121. THE REPORTED STATISTICS REFER TO THE REFINEMENT AGAINST THE TWINNED DATA.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97895, 0.97871
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 18, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.978951
30.978711
ReflectionResolution: 1.9→29.248 Å / Num. obs: 42979 / % possible obs: 89.8 % / Biso Wilson estimate: 28.762 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.26
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
1.9-1.970.3312.6458594161183.8
1.97-2.050.283.5681834386191.2
2.05-2.140.2114.5778894198191.2
2.14-2.250.1835.3280194261191.2
2.25-2.390.1426.7582084342191.3
2.39-2.580.1197.9585734474191
2.58-2.840.08111.1684164378191.1
2.84-3.250.04717.4783714268190.3
3.25-4.080.02828.285014270190
4.08-29.250.235.387844241187.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.248 Å / Num. parameters: 7524 / Num. restraintsaints: 19194 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUES 113-115 IN CHAIN A AND 112-115 IN CHAIN B ARE DISORDERED AND ARE NOT MODELED. 3. REFINEMENT WAS PERFORMED AGAINST INTENSITY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. RESIDUES 113-115 IN CHAIN A AND 112-115 IN CHAIN B ARE DISORDERED AND ARE NOT MODELED. 3. REFINEMENT WAS PERFORMED AGAINST INTENSITY DATA. 4. UNMERGED INTENSITY DATA WAS MERGED WITH SHELXL MERG 2 OPTION (FRIEDEL PAIRS SEPARATE). 5. THE SE FORM FACTORS WERE MODIFIED WITH f' -1.8 and f" 3.4 6. THE DATA ARE PSEUDO-MEROHEDRALLY TWINNED IN SPACE GROUP P212121 WITH THE TWIN LAW -H,L,K. THE REFINED TWIN FRACTION WAS 0.47.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2156 5.02 %THIN SHELL
Rwork0.189 ---
all0.193 42947 --
obs0.193 42947 93.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 26.904 Å2
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1580 / Occupancy sum non hydrogen: 1874
Refinement stepCycle: LAST / Resolution: 1.9→29.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 20 111 1874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0.038
X-RAY DIFFRACTIONs_from_restr_planes0.039
X-RAY DIFFRACTIONs_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0

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