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- PDB-3m92: The structure of yciN, an unchracterized protein from Shigella fl... -

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Basic information

Entry
Database: PDB / ID: 3m92
TitleThe structure of yciN, an unchracterized protein from Shigella flexneri.
ComponentsProtein yciN
Keywordsstructural genomics / unknown function / DUF2498 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function (DUF2498) / Protein of unknown function DUF2498 / YciN superfamily / Protein of unknown function (DUF2498) / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Protein YciN
Function and homology information
Biological speciesShigella flexneri 2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsCuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of yciN, an unchracterized protein from Shigella flexneri.
Authors: Cuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMar 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein yciN
B: Protein yciN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5654
Polymers24,5062
Non-polymers582
Water1,63991
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-42 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.35, 56.35, 132.26
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Detailsunknown but likely dimer in asymmetric unit.

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Components

#1: Protein Protein yciN


Mass: 12253.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 2457T / Gene: S1360, SF1275, yciN / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21 / References: UniProt: P0AB64
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.5M K3PO4, 0.5M NaPO4, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979291
ReflectionRedundancy: 12 % / Av σ(I) over netI: 50.44 / Number: 187426 / Rmerge(I) obs: 0.072 / Χ2: 1.54 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 15604 / % possible obs: 97.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.565087.410.0686.91710.2
4.425.569410.0573.98711.4
3.864.4294.810.063.61111.8
3.513.8696.110.0663.19711.9
3.253.5197.110.0652.50812
3.063.2597.210.0691.85212.2
2.913.0697.810.0721.33912.1
2.782.9197.910.0831.11412.2
2.682.7898.110.0940.88512.1
2.582.6898.210.1150.81212.3
2.52.589910.1340.72612.2
2.432.598.410.1620.65612.2
2.372.439910.1890.60212.2
2.312.3798.510.2060.59212.2
2.262.3199.110.240.56312.3
2.212.2699.310.3310.55412.2
2.162.2198.910.3760.55412
2.122.1699.210.4830.49712.4
2.092.1299.410.6430.48712.1
2.052.0999.510.6550.47612.3
ReflectionResolution: 2.05→50 Å / Num. all: 15604 / Num. obs: 15604 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.541 / Net I/σ(I): 9.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.655 / Num. unique all: 791 / Χ2: 0.476 / % possible all: 99.5

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.05 Å / D res low: 48.8 Å / FOM : 0.301 / FOM acentric: 0.32 / FOM centric: 0.176 / Reflection: 15536 / Reflection acentric: 13472 / Reflection centric: 2064
Phasing MAD set

Highest resolution: 2.05 Å / Lowest resolution: 48.8 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.6310000134722064
20.980.95913.40.390.33125431976
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
112.67-48.81.4910.30.1003229
17.28-12.671.0310.20.20019688
15.11-7.281.5510.20.100509163
13.93-5.111.1710.10.1001001208
13.2-3.931.2610.10001614288
12.7-3.22.35100002386354
12.33-2.710.56100003321419
12.05-2.333.13100004413515
212.67-48.81.07122.322.50.960.953229
27.28-12.670.970.9225.128.80.680.5219688
25.11-7.280.930.911517.90.920.69509163
23.93-5.110.960.931922.20.470.361001208
23.2-3.930.990.9616.520.70.330.231614288
22.7-3.20.980.979.413.10.320.192386354
22.33-2.70.980.985.46.90.290.183320419
22.05-2.330.9913.85.20.210.123485427
Phasing MAD set site

Atom type symbol: Se

IDB isoFract xFract yFract zOccupancyOccupancy iso
163.4469-0.195-0.86-0.0094.7790
266.7653-0.205-0.7980.0464.8940
368.4683-0.322-0.707-0.1381.1140
456.8645-0.194-0.858-0.0092.609-0.21
562.1972-0.204-0.7970.0462.669-0.237
661.387-0.327-0.711-0.1370.505-0.038
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
12.67-48.80.5170.6260.396613229
7.28-12.670.4860.5740.2928419688
5.11-7.280.6140.6790.412672509163
3.93-5.110.520.5750.25412091001208
3.2-3.930.460.5070.19719021614288
2.7-3.20.410.4440.18527402386354
2.33-2.70.2580.2730.13237403321419
2.05-2.330.1020.1080.05449284413515
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15536
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.45-100570.769502
5.12-6.4554.60.89503
4.48-5.1255.10.917506
4.07-4.4858.60.904504
3.77-4.0761.90.916506
3.55-3.7763.20.905503
3.37-3.5559.20.907508
3.22-3.3760.80.893511
3.09-3.2261.80.892516
2.98-3.0959.30.891536
2.88-2.9858.60.882548
2.79-2.8860.60.865568
2.7-2.7962.50.882597
2.63-2.765.30.866631
2.56-2.6366.20.869603
2.49-2.5667.90.87659
2.43-2.4970.40.856642
2.37-2.4371.50.878687
2.32-2.3769.30.886682
2.27-2.3274.40.886717
2.23-2.2774.90.881714
2.18-2.23770.894741
2.14-2.1881.40.894750
2.1-2.1482.20.877753
2.05-2.186.60.8381149

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.05→28.18 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 8.851 / SU ML: 0.11 / SU R Cruickshank DPI: 0.16 / SU Rfree: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.154
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 769 4.9 %RANDOM
Rwork0.198 ---
all0.2 15541 --
obs0.2 15541 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.14 Å2 / Biso mean: 35.166 Å2 / Biso min: 13.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 2 91 1346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221311
X-RAY DIFFRACTIONr_bond_other_d0.0010.02856
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9551783
X-RAY DIFFRACTIONr_angle_other_deg0.92332110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.35824.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18515230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.157156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021462
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_mcbond_it0.8791.5812
X-RAY DIFFRACTIONr_mcbond_other0.211.5331
X-RAY DIFFRACTIONr_mcangle_it1.70421313
X-RAY DIFFRACTIONr_scbond_it2.8623499
X-RAY DIFFRACTIONr_scangle_it4.6454.5465
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 61 -
Rwork0.226 1077 -
all-1138 -
obs--99.3 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.22150.6935-0.37942.1921-0.43612.18840.0832-0.07730.04530.1897-0.1379-0.167-0.12540.19040.05470.172-0.1031-0.04910.07190.04350.140940.098214.71991.8222
22.42450.4812-0.0682.3921-1.22592.732-0.0263-0.0573-0.10040.0564-0.0569-0.12940.05520.02190.08320.1448-0.0874-0.03750.05730.03980.162834.83915.50721.7302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 82
2X-RAY DIFFRACTION1A86
3X-RAY DIFFRACTION1A87 - 125
4X-RAY DIFFRACTION2B2 - 82
5X-RAY DIFFRACTION2B86
6X-RAY DIFFRACTION2B87 - 138

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