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- PDB-3rmq: Crystal structure of uncharacterized protein Svir_20580 from Sacc... -

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Basic information

Entry
Database: PDB / ID: 3rmq
TitleCrystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis (V71M mutant)
Componentsuncharacterized protein
KeywordsStructural Genomics / unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / zinc binding
Function / homology
Function and homology information


Malonyl-[acyl-carrier protein] O-methyltransferase, zinc-finger motif / Helix Hairpins - #1650 / Putative zinc-finger containing protein / zinc-finger / Helix Hairpins / Helix non-globular / Special / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsMichalska, K. / Weger, A. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein Svir_20580 from Saccharomonospora viridis (V71M mutant)
Authors: Michalska, K. / Weger, A. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,53710
Polymers13,1011
Non-polymers4369
Water1,40578
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.225, 79.225, 47.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein uncharacterized protein


Mass: 13101.412 Da / Num. of mol.: 1 / Mutation: V71M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: DSM 43017 / Gene: Svir_20580 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21, pRK1037 / References: UniProt: C7MVX3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8 M NaCl, 0.1 M Tris/HCl, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 10, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 14603 / Num. obs: 14408 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 25.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 2.6 / Num. unique all: 707 / % possible all: 95.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→25.932 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
Details: Hydrogen atoms have been added at ridding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1908 1102 7.65 %random
Rwork0.1617 ---
all0.1639 14402 --
obs0.1639 14402 98.8 %-
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.816 Å2 / ksol: 0.482 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0213 Å2-0 Å20 Å2
2---0.0213 Å2-0 Å2
3---0.0426 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 16 78 970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015941
X-RAY DIFFRACTIONf_angle_d1.3811282
X-RAY DIFFRACTIONf_dihedral_angle_d14.957343
X-RAY DIFFRACTIONf_chiral_restr0.1136
X-RAY DIFFRACTIONf_plane_restr0.007166
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8472-1.93130.24811420.21431644164498
1.9313-2.03310.22111320.17511623162398
2.0331-2.16040.19791510.15791632163299
2.1604-2.32710.18731290.15571675167599
2.3271-2.56110.20411420.16111656165699
2.5611-2.93130.22251350.18621669166999
2.9313-3.69140.1881390.169516731673100
3.6914-25.9350.15261320.13591728172899
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)
11.1320.65530.16890.656-0.09110.16290.07720.02320.01710.1016-0.0646-0.0336-0.04220.0468-0.00550.1394-0.0259-0.0140.1469-0.00190.13194.2905-34.05246.4667
20.53370.9601-0.1962.16530.03840.50180.2219-0.14290.09670.4127-0.22660.1306-0.02740.060.00990.2685-0.0551-0.00830.175-0.02210.17910.0861-30.717212.6263
30.97370.4367-0.14921.4248-0.18790.12710.0363-0.020.01920.0522-0.02270.16380.00650.10660.00070.11760.0099-0.00910.1481-0.0070.1075-3.4849-39.74428.8042
44.0479-0.2060.42532.51830.54330.1731-0.01951.55560.1487-0.8975-0.1433-0.0402-0.36170.09680.10040.36420.0416-0.04010.5147-0.00150.1628-2.977-32.1733-11.3643
52.6469-0.4737-0.23092.5167-1.07672.03260.37720.4406-0.23170.1695-0.3317-0.6202-0.2645-0.427-0.07960.1610.0767-0.01380.19910.0320.2645-10.6832-28.4979-1.6035
63.6653-0.8987-0.33870.6872-0.32890.41380.68821.08420.2594-0.5075-0.486-0.19060.01650.0897-0.11850.33930.16490.08170.42580.11510.3076-12.1633-24.3925-9.0422
72.09332.32914.43763.04395.00939.4769-0.34790.3841-0.34940.1950.030.10370.00990.41710.20880.24360.0640.03370.3324-0.05370.2011-19.9386-31.0991-9.5811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:23)
2X-RAY DIFFRACTION2(chain A and resid 24:39)
3X-RAY DIFFRACTION3(chain A and resid 40:64)
4X-RAY DIFFRACTION4(chain A and resid 65:78)
5X-RAY DIFFRACTION5(chain A and resid 79:96)
6X-RAY DIFFRACTION6(chain A and resid 97:107)
7X-RAY DIFFRACTION7(chain A and resid 108:111)

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