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- PDB-4jpd: The structure of CyaY from Burkholderia cenocepacia -

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Basic information

Entry
Database: PDB / ID: 4jpd
TitleThe structure of CyaY from Burkholderia cenocepacia
ComponentsProtein CyaY
KeywordsMETAL BINDING PROTEIN / SSGCID / Seattle Structural Genomics Center for Infectious Disease / CyaY / Frataxin / iron binding protein
Function / homology
Function and homology information


iron-sulfur cluster assembly / ferric iron binding
Similarity search - Function
Frataxin/CyaY / Metal Transport, Frataxin; Chain A / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Iron-sulfur cluster assembly protein CyaY
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: The structure of CyaY from Burkholderia cenocepacia
Authors: Clifton, M.C. / Davies, D. / Sankaran, B.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

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Assembly

Deposited unit
A: Protein CyaY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4745
Polymers12,2371
Non-polymers2374
Water2,072115
1
A: Protein CyaY
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)74,84230
Polymers73,4196
Non-polymers1,42324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
Buried area16970 Å2
ΔGint-174 kcal/mol
Surface area23440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.020, 96.020, 96.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-203-

NA

21A-204-

SO4

31A-204-

SO4

41A-302-

HOH

51A-311-

HOH

61A-328-

HOH

71A-343-

HOH

81A-412-

HOH

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Components

#1: Protein Protein CyaY


Mass: 12236.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: cyaY, BceJ2315_02750, BCAL0273 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E5Z6
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 50% PEG400, 200mM LiSO4, 100mM Na acetate, 9.46mg/ml BuceA.18084.a.PW33863, direct cryoprotection, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→42.98 Å / Num. obs: 11700 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.707 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 21.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-20.4376.75118458361100
2-2.060.3747.89114258001100
2.06-2.120.3069.74112247871100
2.12-2.180.27410.86109317701100
2.18-2.250.22912.84104327381100
2.25-2.330.21113.74104967391100
2.33-2.420.18814.9897856941100
2.42-2.520.16517.3594456711100
2.52-2.630.14718.9791686501100
2.63-2.760.13619.8787906291100
2.76-2.910.10625.184386031100
2.91-3.080.09227.578225661100
3.08-3.30.08130.7974185391100
3.3-3.560.06337.7768145041100
3.56-3.90.05839.3462084621100
3.9-4.360.0543.3757014401100
4.36-5.040.04647.9150293801100
5.04-6.170.0637.2943493371100
6.17-8.720.0540.8433802731100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.95 Å48.01 Å
Translation1.95 Å48.01 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EW4

1ew4


Resolution: 1.9→42.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1688 / WRfactor Rwork: 0.1405 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8886 / SU B: 3.889 / SU ML: 0.062 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.1108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 584 4.8 %RANDOM
Rwork0.1624 ---
obs0.164 11700 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.81 Å2 / Biso mean: 18.3399 Å2 / Biso min: 4.43 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 14 115 961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019898
X-RAY DIFFRACTIONr_bond_other_d0.0010.02821
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9481234
X-RAY DIFFRACTIONr_angle_other_deg0.77531882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00824.18643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24315135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.889156
X-RAY DIFFRACTIONr_chiral_restr0.0830.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
X-RAY DIFFRACTIONr_mcbond_it0.8950.893451
X-RAY DIFFRACTIONr_mcbond_other0.8690.883448
X-RAY DIFFRACTIONr_mcangle_it1.5481.314563
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 36 -
Rwork0.186 805 -
all-841 -
obs--93.65 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4269-1.59422.31370.7888-0.67381.4161-0.02280.19790.04-0.0179-0.0117-0.033-0.00820.14390.03440.05740.00690.00630.08540.00160.058568.659655.781849.4496
21.1871-0.2859-0.35910.8720.23671.4734-0.02080.0665-0.0483-0.02060.0472-0.05210.13560.0908-0.02630.05190.02570.00690.0554-0.01110.034969.524746.760645.2067
35.03520.1103-2.39420.85262.21237.188-0.267-0.2424-0.13940.12640.09560.03810.50040.48160.17140.13320.1120.02470.13070.05520.043474.459540.559752.8845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 26
2X-RAY DIFFRACTION2A27 - 90
3X-RAY DIFFRACTION3A91 - 108

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