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- PDB-3omd: Crystal structure of unknown function protein from Leptospirillum... -

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Basic information

Entry
Database: PDB / ID: 3omd
TitleCrystal structure of unknown function protein from Leptospirillum rubarum
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG
Function / homology:
Function and homology information
Biological speciesLeptospirillum rubarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Chen, Z. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of unknown function protein from Leptospirillum rubarum
Authors: Chang, C. / Xu, X. / Cui, H. / Chen, Z. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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


Theoretical massNumber of molelcules
Total (without water)34,1972
Polymers34,1972
Non-polymers00
Water6,233346
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,0991
Polymers17,0991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,0991
Polymers17,0991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.910, 66.259, 78.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 17098.645 Da / Num. of mol.: 2 / Fragment: sequence database residues 7-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospirillum rubarum (bacteria) / Gene: UBAL2_82410030 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)gold / References: UniProt: A3EP82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-tris, 1.0M tri-Ammonium Citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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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: Aug 24, 2010
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: 1.5→50 Å / Num. all: 56691 / Num. obs: 54961 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 39
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2671 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.249 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.067
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2793 5.1 %RANDOM
Rwork0.151 ---
all0.1528 54899 --
obs0.1528 54899 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.52 Å2 / Biso mean: 21.3817 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 0 346 2738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212634
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9583595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79223.358137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96615448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2951524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212134
X-RAY DIFFRACTIONr_mcbond_it1.3771.51584
X-RAY DIFFRACTIONr_mcangle_it2.09622586
X-RAY DIFFRACTIONr_scbond_it3.82631050
X-RAY DIFFRACTIONr_scangle_it5.6224.51009
X-RAY DIFFRACTIONr_rigid_bond_restr1.95132634
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 209 -
Rwork0.213 3683 -
all-3892 -
obs-3992 97.23 %
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)
11.2356-0.20120.21610.83050.09351.5142-0.018-0.15550.0160.0057-0.03690.0727-0.0301-0.09910.05490.0360.00530.01230.0298-0.01520.028431.608937.960619.5695
21.78660.3206-0.24181.48070.22142.0059-0.0081-0.12-0.1768-0.02990.0671-0.07110.05580.2376-0.0590.05180.01970.01390.04380.00030.03347.417932.394715.9911
31.2887-0.9380.10282.53380.91651.8099-0.00480.2521-0.0005-0.17220.01440.0242-0.20490.132-0.00960.0592-0.01030.01670.07360.00740.012537.125436.4164-2.3946
41.1781-0.85040.04351.3971-0.30440.72120.03780.019-0.1479-0.0547-0.04210.17210.08280.03350.00420.03020.01650.00650.0708-0.03860.058250.372510.6297-3.4748
51.6432-0.21810.1561.569-1.19684.0740.1020.09250.0680.0807-0.01740.0466-0.2630.0429-0.08460.05060.00480.02980.0418-0.02030.036348.966527.6016-2.5605
61.7311-1.3516-0.62681.2110.71344.4954-0.0378-0.0909-0.08830.0920.11870.0426-0.14590.4989-0.08090.0625-0.00760.00630.0636-0.00170.045853.114119.263617.1616
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 84
2X-RAY DIFFRACTION2A85 - 98
3X-RAY DIFFRACTION3A99 - 140
4X-RAY DIFFRACTION4B-4 - 84
5X-RAY DIFFRACTION5B85 - 98
6X-RAY DIFFRACTION6B99 - 140

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