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- PDB-3iuk: Crystal structure of putative bacterial protein of unknown functi... -

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Basic information

Entry
Database: PDB / ID: 3iuk
TitleCrystal structure of putative bacterial protein of unknown function (DUF885, PF05960.1, ) from Arthrobacter aurescens TC1, reveals fold similar to that of M32 carboxypeptidases
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / PF05960.1 / DUF885 / M32 carboxypeptidase-like fold / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyProtein of unknown function DUF885 / Bacterial protein of unknown function (DUF885) / metal ion binding / DUF885 domain-containing protein
Function and homology information
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsNocek, B. / Chhor, G. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of putative bacterial protein of unknown function (DUF885, PF05960.1, ) from Arthrobacter aurescens TC1, reveals fold similar to that of M32 carboxypeptidases
Authors: Nocek, B. / Chhor, G. / Cobb, G. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9916
Polymers124,8252
Non-polymers1654
Water27,4731525
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5534
Polymers62,4131
Non-polymers1413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4372
Polymers62,4131
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.614, 85.394, 115.489
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein uncharacterized protein


Mass: 62412.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: AAur_1416 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A1R4M8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1525 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 MgCl, 25% Peg3350, 0.1 M Hepes , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794,0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
ReflectionResolution: 1.85→40 Å / Num. all: 98900 / Num. obs: 98606 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 16
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / Num. unique all: 4886 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXmodel building
MLPHAREphasing
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.157 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.135 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21994 4915 5 %RANDOM
Rwork0.16347 ---
all0.168 98246 --
obs0.16633 93331 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.062 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20.12 Å2
2---1.06 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8548 0 9 1525 10082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228801
X-RAY DIFFRACTIONr_bond_other_d0.0010.025949
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.95211967
X-RAY DIFFRACTIONr_angle_other_deg0.991314421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47651115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00523.864427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.748151414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1011572
X-RAY DIFFRACTIONr_chiral_restr0.1010.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021825
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_it0.9021.55494
X-RAY DIFFRACTIONr_mcbond_other0.3031.52247
X-RAY DIFFRACTIONr_mcangle_it1.50928759
X-RAY DIFFRACTIONr_scbond_it2.84633307
X-RAY DIFFRACTIONr_scangle_it4.2724.53200
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 397 -
Rwork0.282 6714 -
obs--97.44 %
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)
11.85451.940.38284.01713.85066.37580.4024-0.3324-0.33530.3843-0.3868-0.23860.4254-0.1403-0.01570.2575-0.0171-0.08190.05880.06570.239816.4887-5.772556.1463
220.51872.8592-4.5774-2.2628-0.6754-1.7629-0.43330.71440.3678-0.00790.407-0.14330.2161-0.31440.02630.4083-0.12930.14230.2638-0.08330.19637.4129-0.45364.7718
36.95140.2207-4.2337-0.62470.07722.8115-0.1809-0.054-0.52720.0309-0.1159-0.05160.2041-0.01870.29680.14430.01840.04250.05890.03030.275317.88247.452967.5413
42.74063.79272.41414.34514.48427.3228-0.18840.1707-0.6426-0.13620.3962-0.67890.2660.9871-0.20780.21280.1280.01940.1559-0.04280.456125.5287-4.343548.6136
51.17511.70910.60232.71961.4881.65950.00140.0328-0.2665-0.00840.1166-0.40460.08360.1543-0.1180.05670.02860.00930.04230.01350.177221.51646.103548.3691
60.89570.6874-0.88491.4896-1.34591.2709-0.07640.0681-0.1215-0.06240.012-0.07930.0796-0.06160.06440.1077-0.02670.01350.0682-0.01050.08996.384411.258970.4058
71.5074-0.1448-0.46151.8837-0.4910.9872-0.0178-0.0145-0.01470.1371-0.095-0.1352-0.07590.08090.11280.0779-0.0206-0.00680.0594-0.00120.073516.924325.738864.6166
82.89362.4453-1.34422.2252-1.52271.28550.1523-0.05350.15390.1961-0.02060.1579-0.1504-0.0151-0.13170.1354-0.00780.0410.0526-0.00570.05852.416316.847879.0468
92.97860.46262.94173.4287-2.562417.9104-0.1101-0.04710.00710.0338-0.2589-0.3604-0.64030.24530.3690.0475-0.02930.00530.0402-0.00690.119619.823333.007862.9792
101.20110.5889-0.29621.6448-0.04741.2334-0.0090.0094-0.0994-0.03920.0007-0.25720.07010.10160.00830.07230.02560.00890.06430.01230.089118.28820.074145.998
112.39730.1720.01680.6821-0.11040.3831-0.08940.07820.1411-0.1220.0591-0.05380.0362-0.00420.03030.09240.00050.00850.07230.02680.0516.656924.053132.826
121.9803-0.14510.45852.4142-1.33344.54860.06170.03750.11510.14860.10060.1563-0.2111-0.2241-0.16230.06930.0434-0.02590.06530.04990.1145-17.662628.630834.9317
131.381-0.6335-0.34121.98250.27660.47910.0159-0.0052-0.0502-0.0698-0.02140.2147-0.0511-0.03560.00560.0927-0.0252-0.00720.07810.00370.0474-15.31923.57442.9828
142.6237-1.04780.18111.2113-1.24870.8842-0.0973-0.25420.21130.39580.0661-0.1252-0.30740.01010.03120.1921-0.01790.00010.1078-0.0250.0538-7.74445.079454.6047
155.6908-5.80840.13838.50471.43590.8338-0.2471-0.29590.11720.58190.18080.10370.1354-0.06540.06620.1635-0.0020.05850.1231-0.01460.0561-12.4219.159354.5888
160.52770.2657-0.25340.6933-0.4960.4019-0.02630.03480.0145-0.030.04420.05840.0112-0.0442-0.01780.0894-0.0074-0.0130.09220.0030.0549-8.05267.645.0952
175.05862.5259-0.08417.201-0.35633.8090.0538-0.0956-0.29280.5352-0.0655-0.180.0054-0.20340.01180.06160.00860.00710.06470.03140.062910.0107-3.276550.3358
180.85440.56420.04920.9772-0.20350.4510.01340.05980.1313-0.10040.00450.03280.0143-0.0384-0.01790.07290.0025-0.00080.06670.01340.05551.354122.526338.3709
191.90890.68680.19913.9118-1.69869.02320.0415-0.05120.17950.0651-0.05770.34380.071-0.41630.01630.0365-0.00560.02370.0497-0.03250.1056-0.369530.78248.9209
200.82420.68410.21612.18130.22680.2891-0.06890.0983-0.0631-0.36750.036-0.21870.02490.0050.03290.1316-0.00530.05470.0604-0.00470.03967.38427.441135.838
214.0686-0.74771.67080.417-1.08132.7882-0.09250.11790.13840.1168-0.1786-0.2256-0.27770.26040.27110.11610.0024-0.04770.11180.04150.148720.03254.842212.491
223.3524-0.3886-0.9776-0.14830.12110.8483-0.00990.22470.29580.02240.0045-0.0474-0.0938-0.11820.00540.10390.0193-0.00060.07970.01290.158527.344744.617819.646
230.4897-0.12010.26670.4051-0.19070.3943-0.0446-0.06320.03380.03510.0015-0.0182-0.0925-0.07920.0430.09240.0322-0.00870.092-0.01040.037711.602344.549613.1297
243.3582.0784-0.95441.7231-0.31350.6174-0.03810.06010.093-0.03070.0766-0.0083-0.0274-0.0127-0.03860.05030.0014-0.01130.06090.02240.086235.465738.679216.7956
250.17340.08740.04881.34220.5290.8896-0.04410.0061-0.09890.00390.1046-0.24010.08620.0375-0.06050.07780.0179-0.00390.07890.00280.107432.279525.128313.5265
263.81962.9497-0.7283.3654-0.52131.26110.02930.1439-0.31150.12230.0601-0.4378-0.01090.141-0.08940.02250.033-0.02250.1048-0.0160.120545.010834.962817.4625
270.9378-1.37461.52671.8628-1.45572.85470.0201-0.0876-0.1257-0.01280.08170.08050.0932-0.1289-0.10180.1069-0.00570.02910.09770.02240.085918.993918.734716.9863
280.6970.71440.98071.87110.35731.7971-0.0496-0.01560.01890.10840.03340.1628-0.021-0.10430.01620.0878-0.00060.01790.0963-0.00550.07046.213630.64932.6603
292.25720.2498-2.66041.9928-0.37855.6707-0.06910.1478-0.0837-0.1440.03160.14690.3874-0.34760.03740.0891-0.057-0.02530.1067-0.02260.03019.897323.8721-19.0613
305.19890.08271.08863.13381.07034.18930.06040.3732-0.2716-0.05520.1676-0.35530.16160.2525-0.22810.118-0.02170.0240.0956-0.07750.064423.355221.4418-27.6954
312.8118-1.0447-0.77372.66110.39561.04880.00970.1124-0.0707-0.1599-0.0125-0.2121-0.08080.06020.00280.0493-0.0236-0.0090.08320.0270.052126.495547.2313-20.6487
321.18670.8081-0.21232.80841.99121.82080.1275-0.1908-0.21620.25810.0416-0.40030.1070.1857-0.16910.0653-0.0165-0.04840.10060.0380.139931.245148.2283-8.2231
335.7822-3.5155-2.28325.16475.37714.8057-0.28580.1578-0.42270.42560.2771-0.01020.39460.36750.00860.12530.0307-0.02070.11970.0240.292336.656135.5292-14.7786
340.60650.0437-0.00482.04391.07050.625-0.03130.07720.0338-0.11980.0818-0.0823-0.04870.0923-0.05050.092-0.0099-0.0070.10150.00810.050222.246844.0581-13.0169
351.15360.7588-0.9076.50731.8454.9870.034-0.0748-0.02810.19750.0668-0.38980.04430.2958-0.10080.02550.019-0.04050.09450.00770.07817.042351.32973.1843
360.51560.3875-0.18480.5446-0.09320.3882-0.06180.0785-0.0253-0.10140.0245-0.00290.08940.00890.03730.0903-0.0168-0.00760.0953-0.00170.039515.010932.4495-14.0777
373.19110.464-2.53652.0676-0.4346.0955-0.260.068-0.2807-0.14980.01680.07770.472-0.22360.24330.0979-0.03060.00690.0472-0.01760.07826.684115.1707-3.9477
384.11931.27030.84851.82380.06331.45390.00640.0584-0.1576-0.1214-0.0442-0.18950.22160.17530.03780.10620.020.02070.05110.01120.065520.162418.0746-3.3681
390.5954-0.53220.23011.6757-0.60710.6705-0.00980.04860.0154-0.0386-0.02080.0746-0.0144-0.09470.03060.05830.0065-0.01980.0957-0.00040.05188.571342.0883-7.7439
401.9046-3.90822.685510.6623-2.80367.3301-0.0537-0.196-0.0199-0.04090.09860.23660.2027-0.533-0.04490.1110.0157-0.02720.11350.0020.07673.702646.7106-1.6311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 31
2X-RAY DIFFRACTION2A32 - 40
3X-RAY DIFFRACTION3A41 - 57
4X-RAY DIFFRACTION4A58 - 75
5X-RAY DIFFRACTION5A76 - 99
6X-RAY DIFFRACTION6A100 - 143
7X-RAY DIFFRACTION7A144 - 174
8X-RAY DIFFRACTION8A175 - 223
9X-RAY DIFFRACTION9A224 - 233
10X-RAY DIFFRACTION10A234 - 251
11X-RAY DIFFRACTION11A252 - 273
12X-RAY DIFFRACTION12A274 - 299
13X-RAY DIFFRACTION13A300 - 339
14X-RAY DIFFRACTION14A340 - 358
15X-RAY DIFFRACTION15A359 - 370
16X-RAY DIFFRACTION16A371 - 402
17X-RAY DIFFRACTION17A403 - 414
18X-RAY DIFFRACTION18A415 - 482
19X-RAY DIFFRACTION19A483 - 502
20X-RAY DIFFRACTION20A503 - 559
21X-RAY DIFFRACTION21B8 - 36
22X-RAY DIFFRACTION22B37 - 57
23X-RAY DIFFRACTION23B58 - 112
24X-RAY DIFFRACTION24B113 - 155
25X-RAY DIFFRACTION25B156 - 186
26X-RAY DIFFRACTION26B187 - 222
27X-RAY DIFFRACTION27B223 - 238
28X-RAY DIFFRACTION28B239 - 263
29X-RAY DIFFRACTION29B264 - 277
30X-RAY DIFFRACTION30B278 - 299
31X-RAY DIFFRACTION31B300 - 339
32X-RAY DIFFRACTION32B340 - 361
33X-RAY DIFFRACTION33B362 - 374
34X-RAY DIFFRACTION34B375 - 402
35X-RAY DIFFRACTION35B403 - 418
36X-RAY DIFFRACTION36B419 - 463
37X-RAY DIFFRACTION37B464 - 475
38X-RAY DIFFRACTION38B476 - 502
39X-RAY DIFFRACTION39B503 - 549
40X-RAY DIFFRACTION40B550 - 559

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