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- PDB-4dci: Crystal structure of unknown funciton protein from Synechococcus ... -

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Basic information

Entry
Database: PDB / ID: 4dci
TitleCrystal structure of unknown funciton protein from Synechococcus sp. WH 8102
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-biology / midwest center for structural genomics / MCSG
Function / homologyHelix Hairpins - #1110 / YlqD protein / YlqD protein / Helix Hairpins / Helix non-globular / Special / Uncharacterized protein
Function and homology information
Biological speciesSynechococcus sp. WH 8102 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.82 Å
AuthorsChang, C. / Marshall, N. / Bearden, J. / Palenik, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein from Synechococcus sp. WH 8102
Authors: Chang, C. / Marshall, N. / Bearden, J. / Palenik, B. / Joachimiak, A.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
E: uncharacterized protein
F: uncharacterized protein
G: uncharacterized protein
H: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,72310
Polymers135,5318
Non-polymers1922
Water1,02757
1
A: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8625
Polymers67,7664
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-66 kcal/mol
Surface area35600 Å2
MethodPISA
2
E: uncharacterized protein
F: uncharacterized protein
G: uncharacterized protein
H: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8625
Polymers67,7664
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-56 kcal/mol
Surface area36340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.272, 164.522, 105.421
Angle α, β, γ (deg.)90.000, 131.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
uncharacterized protein


Mass: 16941.410 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. WH 8102 (bacteria) / Strain: WH8102 / Gene: SYNW0670 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7U8F0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 1.8M Magnesium sulfate, pH 7.9, 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: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.8→91.75 Å / Num. all: 45064 / Num. obs: 44991 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.69 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.82→91.75 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 32.045 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.337
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25154 2272 5.1 %RANDOM
Rwork0.17693 ---
obs0.18063 42712 98.77 %-
all-44984 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.149 Å2
Baniso -1Baniso -2Baniso -3
1-4.42 Å20 Å23.91 Å2
2---5.79 Å20 Å2
3---6.59 Å2
Refinement stepCycle: LAST / Resolution: 2.82→91.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9179 0 10 57 9246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0199224
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.96112447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3551158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.36426.719512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.114151828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7161580
X-RAY DIFFRACTIONr_chiral_restr0.0640.21467
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216932
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr4.2539224
X-RAY DIFFRACTIONr_sphericity_free31.297532
X-RAY DIFFRACTIONr_sphericity_bonded20.4659214
LS refinement shellResolution: 2.817→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 141 -
Rwork0.293 2712 -
obs--87.03 %
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)
10.74020.2668-0.86252.6342-2.02132.1737-0.00990.0721-0.14060.2802-0.1101-0.0471-0.19570.02950.120.2108-0.0162-0.05240.2232-0.07210.1643-20.0358120.9109-1.5911
215.4529-20.809-3.071128.24774.04810.6465-0.16780.071-0.61540.1430.06580.88430.0888-0.06630.10190.24870.004-0.08940.2539-0.04830.156-20.4153143.1852-18.4263
35.1341-2.25652.094319.6025-1.88721.31350.29210.3891-0.0472-0.8153-0.04970.6755-0.08120.2776-0.24240.1888-0.04040.0790.2305-0.00320.1348-33.93169.4357-14.8874
412.3818-14.21872.544222.4756-0.59771.4092-0.5107-0.9123-0.62040.85430.87710.234-0.0012-0.2281-0.36640.2795-0.06640.10510.1619-0.01860.2487-28.6272171.6309-7.1231
58.7468-11.914-5.502518.7396.78423.6639-0.2673-0.40150.37460.56520.4115-0.86550.09980.2905-0.14410.2019-0.0573-0.10180.1524-0.01190.248-13.1399146.2241-12.3692
61.0761-0.0734-1.981.1192-0.53414.0461-0.0524-0.1038-0.04960.06-0.0355-0.00310.07030.23050.08790.14250.0292-0.0080.2455-0.01360.224-15.9716121.0912-2.7159
76.6336-2.2712.95310.8225-0.96771.6334-0.05260.2642-0.12580.0349-0.06210.12530.06930.14170.11470.17350.0122-0.00390.20560.00160.2172-35.2322118.3042-13.7867
83.9599.77164.944252.524714.58686.38140.3636-0.2053-0.06251.3165-0.35860.35390.4736-0.2616-0.0050.0951-0.0017-0.00710.22660.03480.1771-54.0251138.1156-17.7812
914.23685.03925.794926.078711.12125.9276-2.2088-0.69820.28591.45891.03863.73760.08050.38681.17020.70830.20830.15540.3983-0.02030.8217-50.2595165.6572-6.0105
104.96839.01794.335219.734611.75758.28310.3456-0.5297-0.04430.5147-0.51980.11940.18950.04260.17420.1037-0.09790.03290.2667-0.06490.1982-41.5606166.0761-9.0301
115.32069.25478.080532.869317.666515.1434-0.08160.3353-0.2074-0.71810.841-0.9596-0.27020.7352-0.75940.0518-0.0232-0.00310.17510.01750.1948-46.659139.9346-23.7062
120.36690.11540.02710.71980.17760.05-0.02220.108-0.06180.1378-0.0210.15160.0570.02180.04320.1872-0.00660.00510.29550.00920.1944-40.1473117.8879-10.5569
135.268514.2421-0.747645.2071-2.06090.11040.45170.211-0.25883.0022-0.4705-0.3904-0.102-0.0520.01880.6697-0.07280.11180.3606-0.00090.0439-52.8239140.41419.7669
149.962614.1511-1.161433.8361-3.7483.20920.44830.0232-0.51191.1183-0.3787-0.4765-0.1390.3798-0.06960.1102-0.0524-0.05560.18880.010.0583-42.3689167.708116.0444
156.123412.8435-5.604630.1947-11.71275.4138-0.2609-0.0185-0.4123-0.6523-0.0172-0.46360.04670.33780.27810.2151-0.20520.03970.3782-0.09710.1276-43.9397167.29166.4989
169.900510.2152-3.910824.2231-3.06341.6177-0.62230.8589-0.4653-0.47690.37850.39740.2352-0.36540.24380.2506-0.03050.11720.2303-0.03540.1735-58.2489141.185811.5602
171.6010.272-2.57810.1562-0.43554.23430.05360.14590.02520.0752-0.05190.17530.03-0.1849-0.00170.2129-0.03220.12410.2191-0.05890.2952-51.1824117.70022.792
183.58462.96663.50663.29242.51523.7318-0.1283-0.0585-0.08480.2025-0.0269-0.2148-0.1474-0.11740.15520.27940.01080.13220.1746-0.02440.2766-31.6123120.152914.0161
191.2561-5.59441.764325.4583-7.9246.07560.19450.11870.1409-1.2361-0.3041-0.64990.28960.1730.10960.2791-0.1247-0.03660.1358-0.01260.2299-15.1973144.733319.2014
206.6595-9.31910.70347.1681-13.29374.51810.68080.57090.6266-0.9901-1.1965-2.1320.11680.22730.51570.31190.1529-0.04880.1795-0.01360.1744-19.8459173.172610.6771
211.11691.0484-1.44867.20461.05212.8852-0.12340.52960.1227-0.93410.2860.3571-0.0432-0.8039-0.16260.282-0.0372-0.21360.32070.04250.3026-28.4654172.624913.5521
221.3413-6.71222.199233.9119-10.52775.5195-0.1323-0.2568-0.22960.4731.05481.151-0.0117-0.7847-0.92260.25540.002-0.07670.2908-0.00680.3266-22.9612145.334425.1117
235.01190.83993.00411.6874-0.02031.98510.0883-0.1382-0.1150.2985-0.0526-0.0929-0.0477-0.1059-0.03560.26870.02140.08510.18590.00130.0949-30.8549119.781517.7481
242.950.47734.24981.80421.75896.81140.040.03870.1145-0.0824-0.21920.01240.0428-0.0140.17920.12640.02960.04740.32630.04190.1083-10.3709188.724941.5918
2511.8019-21.07583.358551.55-5.96612.02210.0636-0.31470.2728-2.10360.1166-1.1917-0.0201-0.1105-0.18020.29240.0240.11760.2068-0.01560.1089-14.7261168.258121.8184
266.4842-13.5711-1.541629.40395.39635.62790.6796-0.040.2199-1.306-0.0667-0.61340.6431-0.435-0.6130.4913-0.1532-0.13540.09250.07250.2696-3.1748140.5523.4423
2718.2752-18.74227.443620.061-7.22063.2367-0.6367-1.3382-0.5698-0.36451.25480.0278-0.6632-0.5648-0.61821.05730.00750.54960.16960.15470.5271-6.4468139.258932.5155
288.3249-13.1182.42533.303-3.53190.7159-0.4271-0.7776-0.08361.35280.43970.4043-0.0991-0.265-0.01260.2143-0.067-0.03520.2634-0.04810.0583-20.7166166.289429.1329
291.3381-0.38622.17620.49040.12385.05230.029-0.0543-0.1053-0.0767-0.04110.1085-0.0868-0.14520.01210.19190.034-0.01170.206-0.00390.1729-14.2672188.804340.6236
3012.8327-4.4367-8.4571.55513.04186.58910.34690.19830.6501-0.1585-0.1019-0.2407-0.2823-0.3409-0.24510.221-0.01620.13470.1780.00910.2815.5586189.522430.0065
312.81733.1126-0.292645.4652-8.76811.9231-0.0503-0.11660.00171.26920.3155-0.2729-0.2667-0.0967-0.26520.0828-0.00450.01660.2387-0.00530.485223.945167.877323.0458
320.81653.1424-2.66813.7589-11.26879.3657-0.0419-0.0989-0.02110.6556-0.2317-0.6308-0.41550.17150.27360.38740.0771-0.13010.16880.02380.433318.3257139.615531.4614
331.46935.2693-2.852929.5954-9.17755.65750.11140.01830.31571.29610.58450.6356-0.1124-0.0247-0.69590.13450.03-0.02620.20090.06740.20439.0029140.845629.993
342.42917.047-2.773725.2497-7.71693.20580.08820.06280.2655-0.48060.20751.0814-0.1131-0.1053-0.29570.1941-0.0583-0.01810.2494-0.0060.24116.4622167.541417.1033
354.4242-0.226-2.6650.17110.08331.63660.07660.06480.1887-0.1733-0.0335-0.1497-0.0133-0.0676-0.04310.23520.0520.09570.2092-0.00840.19056.4157190.076826.2818
364.3125-2.50424.53591.5857-2.4425.16590.10450.16220.1380.0068-0.0815-0.23330.09130.0893-0.0230.21110.0279-0.0620.1811-0.09120.314218.3724185.031347.6932
377.404114.06854.057438.18799.17562.5354-0.3081-0.16190.20531.12210.31021.33490.09780.0439-0.00210.29650.05130.05280.2195-0.03320.461522.4184161.731161.2109
385.339511.1722.908331.62815.99731.63070.2348-0.25280.43291.1764-0.39570.610.1971-0.12860.16090.2316-0.0215-0.02580.1903-0.02950.326312.7518133.893155.8005
391.41895.26321.038426.37925.98642.6824-0.30030.15810.3444-0.5160.22120.9326-0.0751-0.28030.0790.1725-0.0351-0.07340.1841-0.01130.263915.3688134.286947.0986
4010.724514.86255.343729.40618.29912.7562-0.53350.25370.157-1.09190.48170.2028-0.29550.13610.05180.1521-0.0025-0.0050.2507-0.02130.156828.1223161.22653.469
411.4701-0.72292.6870.6539-1.33334.9399-0.0890.12180.05590.0393-0.0191-0.3139-0.14190.16170.10810.123-0.0034-0.00760.1696-0.05330.321321.0719187.035846.3902
429.37484.4496-6.02162.201-2.73414.5760.0832-0.32690.41750.1-0.00490.19080.23770.3542-0.07820.17050.08640.01960.2616-0.06060.20170.8989185.671957.8771
432.8275-5.1444-3.897535.976414.87917.6538-0.1238-0.0284-0.0546-1.2328-0.23071.0086-0.2609-0.03310.35450.29440.03940.01550.09770.03590.1389-16.0313163.914659.7551
445.35825.09240.78635.02470.72160.1189-0.36530.62750.7795-0.0540.33631.0482-0.08160.12250.02890.7717-0.2430.30140.3502-0.28650.6371-12.639138.101747.1896
451.2071-1.7344-1.311515.702310.48137.1637-0.0698-0.233-0.1695-1.37650.6076-0.6692-0.77340.4558-0.53770.4773-0.01540.230.0562-0.02490.4119-3.8854136.246650.6515
462.4002-4.1432-3.996724.93379.42137.0213-0.1737-0.7520.2446-0.10350.7917-1.65480.19471.1569-0.6180.13610.14210.03860.32370.02990.2582-8.9633161.990666.1422
473.8418-0.0884-2.25481.1050.34671.4068-0.0909-0.2507-0.02590.18790.095-0.12660.07540.1552-0.00410.25510.1148-0.0580.2293-0.02660.11490.8228186.316561.1861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 43
3X-RAY DIFFRACTION3A44 - 62
4X-RAY DIFFRACTION4A63 - 83
5X-RAY DIFFRACTION5A84 - 103
6X-RAY DIFFRACTION6A104 - 144
7X-RAY DIFFRACTION7B2 - 23
8X-RAY DIFFRACTION8B24 - 43
9X-RAY DIFFRACTION9B44 - 62
10X-RAY DIFFRACTION10B63 - 83
11X-RAY DIFFRACTION11B84 - 103
12X-RAY DIFFRACTION12B104 - 144
13X-RAY DIFFRACTION12C2 - 23
14X-RAY DIFFRACTION13C24 - 43
15X-RAY DIFFRACTION14C44 - 62
16X-RAY DIFFRACTION15C63 - 83
17X-RAY DIFFRACTION16C84 - 103
18X-RAY DIFFRACTION17C104 - 144
19X-RAY DIFFRACTION18D2 - 23
20X-RAY DIFFRACTION19D24 - 43
21X-RAY DIFFRACTION20D44 - 62
22X-RAY DIFFRACTION21D63 - 83
23X-RAY DIFFRACTION22D84 - 103
24X-RAY DIFFRACTION23D104 - 144
25X-RAY DIFFRACTION24E2 - 23
26X-RAY DIFFRACTION25E24 - 43
27X-RAY DIFFRACTION26E44 - 62
28X-RAY DIFFRACTION27E63 - 83
29X-RAY DIFFRACTION28E84 - 103
30X-RAY DIFFRACTION29E104 - 144
31X-RAY DIFFRACTION30F2 - 23
32X-RAY DIFFRACTION31F24 - 43
33X-RAY DIFFRACTION32F44 - 62
34X-RAY DIFFRACTION33F63 - 83
35X-RAY DIFFRACTION34F84 - 103
36X-RAY DIFFRACTION35F104 - 144
37X-RAY DIFFRACTION36G2 - 23
38X-RAY DIFFRACTION37G24 - 43
39X-RAY DIFFRACTION38G44 - 62
40X-RAY DIFFRACTION39G63 - 83
41X-RAY DIFFRACTION40G84 - 103
42X-RAY DIFFRACTION41G104 - 144
43X-RAY DIFFRACTION42H2 - 23
44X-RAY DIFFRACTION43H24 - 43
45X-RAY DIFFRACTION44H44 - 62
46X-RAY DIFFRACTION45H63 - 83
47X-RAY DIFFRACTION46H84 - 103
48X-RAY DIFFRACTION47H104 - 144

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